Hi Ben,

I’m learning it myself too.

I played it a little more. I see the mismatch can happen if you skip a number in you LUT.

Also, if you have ‘0 Unknown 0 0 0 0’ in your LUT, I’m not sure you should use ‘--no-unknown’ for mris_label2annot. It will cause your annotation off by one.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Benjamin Deck Sent: Thursday, June 16, 2022 10:58 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

Thanks for taking a look. What do you mean by mismatch?

The LUT was used to make the annot file. What would generate this mismatch?

Here is the output from my mris_label2annot call:

mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --hemi lh Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 105 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 1 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_10_ROIs_1_lh_native.label 2 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_11_ROIs_1_lh_native.label 3 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_1_lh_native.label 4 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_2_lh_native.label 5 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_1_lh_native.label 6 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_2_lh_native.label 7 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_3_lh_native.label 8 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_4_lh_native.label 9 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_5_lh_native.label 10 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_1_lh_native.label 11 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_2_lh_native.label 12 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_3_lh_native.label 13 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_4_lh_native.label 14 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_5_lh_native.label 15 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_15_ROIs_1_lh_native.label 16 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_1_lh_native.label 17 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_2_lh_native.label 18 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_1_lh_native.label 19 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_2_lh_native.label 20 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_3_lh_native.label 21 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_4_lh_native.label 22 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_1_lh_native.label 23 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_2_lh_native.label 24 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_3_lh_native.label 25 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_4_lh_native.label 26 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_5_lh_native.label 27 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_19_ROIs_1_lh_native.label 28 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_1_lh_native.label 29 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_2_lh_native.label 30 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_1_lh_native.label 31 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_2_lh_native.label 32 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_3_lh_native.label 33 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_4_ROIs_1_lh_native.label 34 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_1_lh_native.label 35 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_2_lh_native.label 36 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_3_lh_native.label 37 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_4_lh_native.label 38 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_1_lh_native.label 39 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_2_lh_native.label 40 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_3_lh_native.label 41 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_1_lh_native.label 42 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_2_lh_native.label 43 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_1_lh_native.label 44 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_2_lh_native.label 45 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_3_lh_native.label 46 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_4_lh_native.label 47 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_5_lh_native.label 48 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_1_lh_native.label 49 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_2_lh_native.label 50 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_3_lh_native.label

7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --hemi lh sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 50 LabelThresh 0 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig 0 1336330 Net_10_ROIs_1_lh_native 1 1639705 Net_11_ROIs_1_lh_native 2 2647065 Net_12_ROIs_1_lh_native 3 11829830 Net_12_ROIs_2_lh_native 4 25700 Net_13_ROIs_1_lh_native 5 16399044 Net_13_ROIs_2_lh_native 6 6500 Net_13_ROIs_3_lh_native 7 3294840 Net_13_ROIs_4_lh_native 8 660700 Net_13_ROIs_5_lh_native 9 6558940 Net_14_ROIs_1_lh_native 10 7874740 Net_14_ROIs_2_lh_native 11 14465658 Net_14_ROIs_3_lh_native 12 9180300 Net_14_ROIs_4_lh_native 13 12300 Net_14_ROIs_5_lh_native 14 9182740 Net_15_ROIs_1_lh_native 15 3296035 Net_16_ROIs_1_lh_native 16 9211105 Net_16_ROIs_2_lh_native 17 4924360 Net_17_ROIs_1_lh_native 18 3302560 Net_17_ROIs_2_lh_native 19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native 21 13777468 Net_18_ROIs_1_lh_native 22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native 24 3294765 Net_18_ROIs_4_lh_native 25 14443610 Net_18_ROIs_5_lh_native 26 10511400 Net_19_ROIs_1_lh_native 27 8323072 Net_2_ROIs_1_lh_native 28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native 30 1316060 Net_3_ROIs_2_lh_native 31 14464220 Net_3_ROIs_3_lh_native 32 8323072 Net_4_ROIs_1_lh_native 33 7874740 Net_5_ROIs_1_lh_native 34 9180300 Net_5_ROIs_2_lh_native 35 8860211 Net_5_ROIs_3_lh_native 36 9182740 Net_5_ROIs_4_lh_native 37 3296035 Net_6_ROIs_1_lh_native 38 9211105 Net_6_ROIs_2_lh_native 39 4924360 Net_6_ROIs_3_lh_native 40 3302560 Net_7_ROIs_1_lh_native 41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native 45 3302620 Net_8_ROIs_4_lh_native 46 10811612 Net_8_ROIs_5_lh_native 47 2637020 Net_9_ROIs_1_lh_native 48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot

Thanks,

Ben

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On Tue, Jun 14, 2022 at 1:33 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,

I was able to reproduce the core dump. In my case, it was because a mismatch of color scheme between input annotation file and the color table loaded with the surface.

I suspect it might be the same issue for you too. But I’m not sure what the right action is to work around this.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Friday, June 10, 2022 11:47 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi there,

Having issues with the following command:

mri_label2vol --annot lh.yeo_2011.annot --temp /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz --hemi lh --fill-ribbon --identity --subject sub-DAEK --o lh.sub-DAEK_annot_nat.nii.gz

produces the following error:

Number of labels: 0 Annot File: lh.yeo_2011.annot Template Volume: /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz Outut Volume: lh.sub-DAEK_annot_nat.nii.gz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: sub-DAEK Hemi: lh UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects 7.2.0 Template RAS-to-Vox: -------- -1.25000 -0.00000 -0.00000 160.00000; -0.00000 -0.00000 -1.25000 160.00000; -0.00000 1.25000 -0.00000 160.00000; -0.00000 -0.00000 -0.00000 1.00000; Template Voxel Volume: 0.512 nHits Thresh: 0 Using Identity Matrix RegMat: -------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Label RAS-to-Vox: -------- -1.25000 0.00000 0.00000 160.00000; 0.00000 0.00000 -1.25000 160.00000; 0.00000 1.25000 0.00000 160.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.white nvertices = 253237 Reading thickness /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.thickness Loading annotations from lh.yeo_2011.annot annotidmax = 48 nlabels = 48 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgz Mapping Segmentation fault

But when I run the same command without fill-ribbon the process runs to completion.

Not sure if this is a memory issue or something else.

Ben

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University

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-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University

External Email - Use Caution

Hi Yujing,

Thank you. I will give it a try! Can documentation be updated?

Ben

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On Fri, Jun 17, 2022 at 2:56 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

Hi Ben,

Just wanted to update you on mris_label2annot command line options.

If ‘--no-unknown’ is used with mris_label2annot, ‘—offset 1’ should also be specified.

Yujing

*From:* Huang, Yujing *Sent:* Thursday, June 16, 2022 1:59 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* RE: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

Hi Ben,

I’m learning it myself too.

I played it a little more. I see the mismatch can happen if you skip a number in you LUT.

Also, if you have ‘0 Unknown 0 0 0 0’ in your LUT, I’m not sure you should use ‘--no-unknown’ for mris_label2annot. It will cause your annotation off by one.

Yujing

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Benjamin Deck *Sent:* Thursday, June 16, 2022 10:58 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

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Hi Yujing,

Thanks for taking a look. What do you mean by mismatch?

The LUT was used to make the annot file. What would generate this mismatch?

Here is the output from my mris_label2annot call:

mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --hemi lh Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 105 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 1 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_10_ROIs_1_lh_native.label 2 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_11_ROIs_1_lh_native.label 3 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_1_lh_native.label 4 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_2_lh_native.label 5 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_1_lh_native.label 6 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_2_lh_native.label 7 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_3_lh_native.label 8 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_4_lh_native.label 9 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_5_lh_native.label 10 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_1_lh_native.label 11 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_2_lh_native.label 12 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_3_lh_native.label 13 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_4_lh_native.label 14 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_5_lh_native.label 15 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_15_ROIs_1_lh_native.label 16 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_1_lh_native.label 17 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_2_lh_native.label 18 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_1_lh_native.label 19 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_2_lh_native.label 20 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_3_lh_native.label 21 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_4_lh_native.label 22 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_1_lh_native.label 23 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_2_lh_native.label 24 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_3_lh_native.label 25 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_4_lh_native.label 26 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_5_lh_native.label 27 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_19_ROIs_1_lh_native.label 28 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_1_lh_native.label 29 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_2_lh_native.label 30 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_1_lh_native.label 31 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_2_lh_native.label 32 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_3_lh_native.label 33 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_4_ROIs_1_lh_native.label 34 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_1_lh_native.label 35 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_2_lh_native.label 36 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_3_lh_native.label 37 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_4_lh_native.label 38 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_1_lh_native.label 39 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_2_lh_native.label 40 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_3_lh_native.label 41 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_1_lh_native.label 42 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_2_lh_native.label 43 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_1_lh_native.label 44 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_2_lh_native.label 45 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_3_lh_native.label 46 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_4_lh_native.label 47 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_5_lh_native.label 48 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_1_lh_native.label 49 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_2_lh_native.label 50 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_3_lh_native.label

7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --hemi lh sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 50 LabelThresh 0 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig 0 1336330 Net_10_ROIs_1_lh_native 1 1639705 Net_11_ROIs_1_lh_native 2 2647065 Net_12_ROIs_1_lh_native 3 11829830 Net_12_ROIs_2_lh_native 4 25700 Net_13_ROIs_1_lh_native 5 16399044 Net_13_ROIs_2_lh_native 6 6500 Net_13_ROIs_3_lh_native 7 3294840 Net_13_ROIs_4_lh_native 8 660700 Net_13_ROIs_5_lh_native 9 6558940 Net_14_ROIs_1_lh_native 10 7874740 Net_14_ROIs_2_lh_native 11 14465658 Net_14_ROIs_3_lh_native 12 9180300 Net_14_ROIs_4_lh_native 13 12300 Net_14_ROIs_5_lh_native 14 9182740 Net_15_ROIs_1_lh_native 15 3296035 Net_16_ROIs_1_lh_native 16 9211105 Net_16_ROIs_2_lh_native 17 4924360 Net_17_ROIs_1_lh_native 18 3302560 Net_17_ROIs_2_lh_native 19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native 21 13777468 Net_18_ROIs_1_lh_native 22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native 24 3294765 Net_18_ROIs_4_lh_native 25 14443610 Net_18_ROIs_5_lh_native 26 10511400 Net_19_ROIs_1_lh_native 27 8323072 Net_2_ROIs_1_lh_native 28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native 30 1316060 Net_3_ROIs_2_lh_native 31 14464220 Net_3_ROIs_3_lh_native 32 8323072 Net_4_ROIs_1_lh_native 33 7874740 Net_5_ROIs_1_lh_native 34 9180300 Net_5_ROIs_2_lh_native 35 8860211 Net_5_ROIs_3_lh_native 36 9182740 Net_5_ROIs_4_lh_native 37 3296035 Net_6_ROIs_1_lh_native 38 9211105 Net_6_ROIs_2_lh_native 39 4924360 Net_6_ROIs_3_lh_native 40 3302560 Net_7_ROIs_1_lh_native 41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native 45 3302620 Net_8_ROIs_4_lh_native 46 10811612 Net_8_ROIs_5_lh_native 47 2637020 Net_9_ROIs_1_lh_native 48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot

Thanks,

Ben

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On Tue, Jun 14, 2022 at 1:33 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

Hi Ben,

I was able to reproduce the core dump. In my case, it was because a mismatch of color scheme between input annotation file and the color table loaded with the surface.

I suspect it might be the same issue for you too. But I’m not sure what the right action is to work around this.

Yujing

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Benjamin Deck *Sent:* Friday, June 10, 2022 11:47 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] mri_label2vol fill-ribbon segmentation fault

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Hi there,

Having issues with the following command:

mri_label2vol --annot lh.yeo_2011.annot --temp /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz --hemi lh --fill-ribbon --identity --subject sub-DAEK --o lh.sub-DAEK_annot_nat.nii.gz

produces the following error:

Number of labels: 0 Annot File: lh.yeo_2011.annot Template Volume: /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz Outut Volume: lh.sub-DAEK_annot_nat.nii.gz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: sub-DAEK Hemi: lh UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects 7.2.0 Template RAS-to-Vox: -------- -1.25000 -0.00000 -0.00000 160.00000; -0.00000 -0.00000 -1.25000 160.00000; -0.00000 1.25000 -0.00000 160.00000; -0.00000 -0.00000 -0.00000 1.00000; Template Voxel Volume: 0.512 nHits Thresh: 0 Using Identity Matrix RegMat: -------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Label RAS-to-Vox: -------- -1.25000 0.00000 0.00000 160.00000; 0.00000 0.00000 -1.25000 160.00000; 0.00000 1.25000 0.00000 160.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.white nvertices = 253237 Reading thickness /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.thickness Loading annotations from lh.yeo_2011.annot annotidmax = 48 nlabels = 48 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgz Mapping Segmentation fault

But when I run the same command without fill-ribbon the process runs to completion.

Not sure if this is a memory issue or something else.

Ben

--

*Benjamin L. Deck*

*Doctoral Student*

*Applied Cognitive and Brain Sciences*

*Department of Psychological and Brain Sciences*

*Drexel University*

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*Applied Cognitive and Brain Sciences*

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Hi Ben,

Do you mean the issue that ‘mri_label2vol –fill-ribbon’ crashes? Can you re-run and provide your mris_label2annot and mri_label2vol command line and output?

I’m not sure I will be able to offer work around, but I would like to understand the problem better for future development.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Benjamin Deck Sent: Tuesday, June 21, 2022 5:04 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

It seems that this did not solve the issue. Are there any other reasons why this would occur?

Ben

On Fri, Jun 17, 2022 at 2:59 PM Benjamin Deck <bdeck8317@gmail.commailto:bdeck8317@gmail.com> wrote: Hi Yujing,

Thank you. I will give it a try! Can documentation be updated?

Ben

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On Fri, Jun 17, 2022 at 2:56 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,

Just wanted to update you on mris_label2annot command line options.

If ‘--no-unknown’ is used with mris_label2annot, ‘—offset 1’ should also be specified.

Yujing

From: Huang, Yujing Sent: Thursday, June 16, 2022 1:59 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: RE: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

Hi Ben,

I’m learning it myself too.

I played it a little more. I see the mismatch can happen if you skip a number in you LUT.

Also, if you have ‘0 Unknown 0 0 0 0’ in your LUT, I’m not sure you should use ‘--no-unknown’ for mris_label2annot. It will cause your annotation off by one.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Thursday, June 16, 2022 10:58 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

Thanks for taking a look. What do you mean by mismatch?

The LUT was used to make the annot file. What would generate this mismatch?

Here is the output from my mris_label2annot call:

mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --hemi lh Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 105 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 1 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_10_ROIs_1_lh_native.label 2 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_11_ROIs_1_lh_native.label 3 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_1_lh_native.label 4 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_2_lh_native.label 5 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_1_lh_native.label 6 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_2_lh_native.label 7 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_3_lh_native.label 8 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_4_lh_native.label 9 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_5_lh_native.label 10 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_1_lh_native.label 11 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_2_lh_native.label 12 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_3_lh_native.label 13 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_4_lh_native.label 14 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_5_lh_native.label 15 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_15_ROIs_1_lh_native.label 16 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_1_lh_native.label 17 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_2_lh_native.label 18 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_1_lh_native.label 19 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_2_lh_native.label 20 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_3_lh_native.label 21 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_4_lh_native.label 22 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_1_lh_native.label 23 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_2_lh_native.label 24 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_3_lh_native.label 25 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_4_lh_native.label 26 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_5_lh_native.label 27 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_19_ROIs_1_lh_native.label 28 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_1_lh_native.label 29 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_2_lh_native.label 30 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_1_lh_native.label 31 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_2_lh_native.label 32 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_3_lh_native.label 33 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_4_ROIs_1_lh_native.label 34 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_1_lh_native.label 35 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_2_lh_native.label 36 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_3_lh_native.label 37 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_4_lh_native.label 38 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_1_lh_native.label 39 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_2_lh_native.label 40 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_3_lh_native.label 41 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_1_lh_native.label 42 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_2_lh_native.label 43 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_1_lh_native.label 44 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_2_lh_native.label 45 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_3_lh_native.label 46 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_4_lh_native.label 47 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_5_lh_native.label 48 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_1_lh_native.label 49 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_2_lh_native.label 50 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_3_lh_native.label

7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --hemi lh sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 50 LabelThresh 0 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig 0 1336330 Net_10_ROIs_1_lh_native 1 1639705 Net_11_ROIs_1_lh_native 2 2647065 Net_12_ROIs_1_lh_native 3 11829830 Net_12_ROIs_2_lh_native 4 25700 Net_13_ROIs_1_lh_native 5 16399044 Net_13_ROIs_2_lh_native 6 6500 Net_13_ROIs_3_lh_native 7 3294840 Net_13_ROIs_4_lh_native 8 660700 Net_13_ROIs_5_lh_native 9 6558940 Net_14_ROIs_1_lh_native 10 7874740 Net_14_ROIs_2_lh_native 11 14465658 Net_14_ROIs_3_lh_native 12 9180300 Net_14_ROIs_4_lh_native 13 12300 Net_14_ROIs_5_lh_native 14 9182740 Net_15_ROIs_1_lh_native 15 3296035 Net_16_ROIs_1_lh_native 16 9211105 Net_16_ROIs_2_lh_native 17 4924360 Net_17_ROIs_1_lh_native 18 3302560 Net_17_ROIs_2_lh_native 19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native 21 13777468 Net_18_ROIs_1_lh_native 22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native 24 3294765 Net_18_ROIs_4_lh_native 25 14443610 Net_18_ROIs_5_lh_native 26 10511400 Net_19_ROIs_1_lh_native 27 8323072 Net_2_ROIs_1_lh_native 28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native 30 1316060 Net_3_ROIs_2_lh_native 31 14464220 Net_3_ROIs_3_lh_native 32 8323072 Net_4_ROIs_1_lh_native 33 7874740 Net_5_ROIs_1_lh_native 34 9180300 Net_5_ROIs_2_lh_native 35 8860211 Net_5_ROIs_3_lh_native 36 9182740 Net_5_ROIs_4_lh_native 37 3296035 Net_6_ROIs_1_lh_native 38 9211105 Net_6_ROIs_2_lh_native 39 4924360 Net_6_ROIs_3_lh_native 40 3302560 Net_7_ROIs_1_lh_native 41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native 45 3302620 Net_8_ROIs_4_lh_native 46 10811612 Net_8_ROIs_5_lh_native 47 2637020 Net_9_ROIs_1_lh_native 48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot

Thanks,

Ben

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On Tue, Jun 14, 2022 at 1:33 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,

I was able to reproduce the core dump. In my case, it was because a mismatch of color scheme between input annotation file and the color table loaded with the surface.

I suspect it might be the same issue for you too. But I’m not sure what the right action is to work around this.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Friday, June 10, 2022 11:47 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi there,

Having issues with the following command:

mri_label2vol --annot lh.yeo_2011.annot --temp /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz --hemi lh --fill-ribbon --identity --subject sub-DAEK --o lh.sub-DAEK_annot_nat.nii.gz

produces the following error:

Number of labels: 0 Annot File: lh.yeo_2011.annot Template Volume: /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz Outut Volume: lh.sub-DAEK_annot_nat.nii.gz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: sub-DAEK Hemi: lh UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects 7.2.0 Template RAS-to-Vox: -------- -1.25000 -0.00000 -0.00000 160.00000; -0.00000 -0.00000 -1.25000 160.00000; -0.00000 1.25000 -0.00000 160.00000; -0.00000 -0.00000 -0.00000 1.00000; Template Voxel Volume: 0.512 nHits Thresh: 0 Using Identity Matrix RegMat: -------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Label RAS-to-Vox: -------- -1.25000 0.00000 0.00000 160.00000; 0.00000 0.00000 -1.25000 160.00000; 0.00000 1.25000 0.00000 160.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.white nvertices = 253237 Reading thickness /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.thickness Loading annotations from lh.yeo_2011.annot annotidmax = 48 nlabels = 48 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgz Mapping Segmentation fault

But when I run the same command without fill-ribbon the process runs to completion.

Not sure if this is a memory issue or something else.

Ben

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University

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-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University

How does your LUT look like? What is your first line?

For left hemi, your loaded 50 label files to mris_label2annot, but mri_label2vol only reported 48 labels. It looks like you have duplicated RGB in your LUT. I have identified some. See highlighted in red. The duplicated RGB entries can cause problems.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Benjamin Deck Sent: Wednesday, June 22, 2022 2:24 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

Sure thing.

Commands:

mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt

Output: Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 105 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 1 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_10_ROIs_1_lh_native.label 2 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_11_ROIs_1_lh_native.label 3 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_1_lh_native.label 4 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_2_lh_native.label 5 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_1_lh_native.label 6 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_2_lh_native.label 7 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_3_lh_native.label 8 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_4_lh_native.label 9 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_5_lh_native.label 10 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_1_lh_native.label 11 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_2_lh_native.label 12 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_3_lh_native.label 13 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_4_lh_native.label 14 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_5_lh_native.label 15 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_15_ROIs_1_lh_native.label 16 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_1_lh_native.label 17 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_2_lh_native.label 18 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_1_lh_native.label 19 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_2_lh_native.label 20 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_3_lh_native.label 21 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_4_lh_native.label 22 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_1_lh_native.label 23 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_2_lh_native.label 24 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_3_lh_native.label 25 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_4_lh_native.label 26 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_5_lh_native.label 27 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_19_ROIs_1_lh_native.label 28 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_1_lh_native.label 29 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_2_lh_native.label 30 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_1_lh_native.label 31 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_2_lh_native.label 32 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_3_lh_native.label 33 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_4_ROIs_1_lh_native.label 34 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_1_lh_native.label 35 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_2_lh_native.label 36 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_3_lh_native.label 37 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_4_lh_native.label 38 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_1_lh_native.label 39 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_2_lh_native.label 40 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_3_lh_native.label 41 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_1_lh_native.label 42 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_2_lh_native.label 43 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_1_lh_native.label 44 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_2_lh_native.label 45 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_3_lh_native.label 46 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_4_lh_native.label 47 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_5_lh_native.label 48 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_1_lh_native.label 49 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_2_lh_native.label 50 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_3_lh_native.label

7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 50 LabelThresh 1 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig 0 16777215 Net_10_ROIs_1_lh_native 1 1639705 Net_11_ROIs_1_lh_native 2 2647065 Net_12_ROIs_1_lh_native 3 11829830 Net_12_ROIs_2_lh_native 4 25700 Net_13_ROIs_1_lh_native 5 16399044 Net_13_ROIs_2_lh_native 6 6500 Net_13_ROIs_3_lh_native 7 3294840 Net_13_ROIs_4_lh_native 8 660700 Net_13_ROIs_5_lh_native 9 6558940 Net_14_ROIs_1_lh_native 10 7874740 Net_14_ROIs_2_lh_native 11 14465658 Net_14_ROIs_3_lh_native 12 9180300 Net_14_ROIs_4_lh_native 13 12300 Net_14_ROIs_5_lh_native 14 9182740 Net_15_ROIs_1_lh_native 15 3296035 Net_16_ROIs_1_lh_native 16 9211105 Net_16_ROIs_2_lh_native 17 4924360 Net_17_ROIs_1_lh_native 18 3302560 Net_17_ROIs_2_lh_native 19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native 21 13777468 Net_18_ROIs_1_lh_native 22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native 24 3294765 Net_18_ROIs_4_lh_native 25 14443610 Net_18_ROIs_5_lh_native 26 10511400 Net_19_ROIs_1_lh_native 27 8323072 Net_2_ROIs_1_lh_native 28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native 30 1316060 Net_3_ROIs_2_lh_native 31 14464220 Net_3_ROIs_3_lh_native 32 8323072 Net_4_ROIs_1_lh_native 33 7874740 Net_5_ROIs_1_lh_native 34 9180300 Net_5_ROIs_2_lh_native 35 8860211 Net_5_ROIs_3_lh_native 36 9182740 Net_5_ROIs_4_lh_native 37 3296035 Net_6_ROIs_1_lh_native 38 9211105 Net_6_ROIs_2_lh_native 39 4924360 Net_6_ROIs_3_lh_native 40 3302560 Net_7_ROIs_1_lh_native 41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native 45 3302620 Net_8_ROIs_4_lh_native 46 10811612 Net_8_ROIs_5_lh_native 47 2637020 Net_9_ROIs_1_lh_native 48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot

command: mris_label2annot --s sub-DAEK --hemi rh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt

output: Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 105 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 51 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_10_ROIs_1_rh_native.label 52 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_11_ROIs_1_rh_native.label 53 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_12_ROIs_1_rh_native.label 54 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_12_ROIs_2_rh_native.label 55 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_1_rh_native.label 56 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_2_rh_native.label 57 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_3_rh_native.label 58 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_4_rh_native.label 59 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_1_rh_native.label 60 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_2_rh_native.label 61 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_3_rh_native.label 62 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_4_rh_native.label 63 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_5_rh_native.label 64 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_15_ROIs_1_rh_native.label 65 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_1_rh_native.label 66 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_2_rh_native.label 67 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_3_rh_native.label 68 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_1_rh_native.label 69 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_2_rh_native.label 70 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_3_rh_native.label 71 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_4_rh_native.label 72 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_1_rh_native.label 73 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_2_rh_native.label 74 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_3_rh_native.label 75 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_4_rh_native.label 76 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_19_ROIs_1_rh_native.label 77 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_2_ROIs_1_rh_native.label 78 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_2_ROIs_2_rh_native.label 79 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_1_rh_native.label 80 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_2_rh_native.label 81 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_3_rh_native.label 82 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_4_ROIs_1_rh_native.label 83 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_1_rh_native.label 84 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_2_rh_native.label 85 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_3_rh_native.label 86 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_4_rh_native.label 87 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_1_rh_native.label 88 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_2_rh_native.label 89 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_3_rh_native.label 90 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_1_rh_native.label 91 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_2_rh_native.label 92 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_3_rh_native.label 93 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_1_rh_native.label 94 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_2_rh_native.label 95 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_3_rh_native.label 96 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_4_rh_native.label 97 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_5_rh_native.label 98 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_6_rh_native.label 99 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_1_rh_native.label 100 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_2_rh_native.label 101 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_3_rh_native.label 102 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_4_rh_native.label 103 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_5_rh_native.label 104 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_6_rh_native.label

7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --hemi rh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi rh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 54 LabelThresh 1 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/rh.orig 0 1316060 Net_10_ROIs_1_rh_native 1 14464220 Net_11_ROIs_1_rh_native 2 14423100 Net_12_ROIs_1_rh_native 3 11832480 Net_12_ROIs_2_rh_native 4 9180240 Net_13_ROIs_1_rh_native 5 8204875 Net_13_ROIs_2_rh_native 6 10542100 Net_13_ROIs_3_rh_native 7 9231380 Net_13_ROIs_4_rh_native 8 9221140 Net_14_ROIs_1_rh_native 9 14474380 Net_14_ROIs_2_rh_native 10 2763429 Net_14_ROIs_3_rh_native 11 1351760 Net_14_ROIs_4_rh_native 12 15736992 Net_14_ROIs_5_rh_native 13 6553700 Net_15_ROIs_1_rh_native 14 11146310 Net_16_ROIs_1_rh_native 15 13145750 Net_16_ROIs_2_rh_native 16 3311482 Net_16_ROIs_3_rh_native 17 2146304 Net_17_ROIs_1_rh_native 18 5935475 Net_17_ROIs_2_rh_native 19 681085 Net_17_ROIs_3_rh_native 20 23060 Net_17_ROIs_4_rh_native 21 3957760 Net_18_ROIs_1_rh_native 22 3311482 Net_18_ROIs_2_rh_native 23 1321040 Net_18_ROIs_3_rh_native 24 3276922 Net_18_ROIs_4_rh_native 25 6588260 Net_19_ROIs_1_rh_native 26 3957760 Net_2_ROIs_1_rh_native 27 50372 Net_2_ROIs_2_rh_native 28 2671812 Net_3_ROIs_1_rh_native 29 3957956 Net_3_ROIs_2_rh_native 30 6564036 Net_3_ROIs_3_rh_native 31 3945156 Net_4_ROIs_1_rh_native 32 13127690 Net_5_ROIs_1_rh_native 33 6604880 Net_5_ROIs_2_rh_native 34 2647140 Net_5_ROIs_3_rh_native 35 3937480 Net_5_ROIs_4_rh_native 36 665610 Net_6_ROIs_1_rh_native 37 50372 Net_6_ROIs_2_rh_native 38 706590 Net_6_ROIs_3_rh_native 39 5923840 Net_7_ROIs_1_rh_native 40 6579200 Net_7_ROIs_2_rh_native 41 32768 Net_7_ROIs_3_rh_native 42 25600 Net_8_ROIs_1_rh_native 43 13117500 Net_8_ROIs_2_rh_native 44 6574090 Net_8_ROIs_3_rh_native 45 51200 Net_8_ROIs_4_rh_native 46 8320 Net_8_ROIs_5_rh_native 47 25750 Net_8_ROIs_6_rh_native 48 1336330 Net_9_ROIs_1_rh_native 49 25740 Net_9_ROIs_2_rh_native 50 3983360 Net_9_ROIs_3_rh_native 51 7895160 Net_9_ROIs_4_rh_native 52 6553720 Net_9_ROIs_5_rh_native 53 8312 Net_9_ROIs_6_rh_native Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/rh.yeo2011.annot

---Annotations look fine.

Command: mri_label2vol --o lh.yeo2011_in_nat.mgz --annot ../lh.yeo2011.annot --identity --fill-ribbon --subject sub-DAEK --h emi lh

Output: Number of labels: 0 Annot File: ../lh.yeo2011.annot Template Volume: (null) Outut Volume: lh.yeo2011_in_nat.mgz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: sub-DAEK Hemi: lh UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects 7.2.0 INFO: loading surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.white nvertices = 253237 Reading thickness /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.thickness Loading annotations from ../lh.yeo2011.annot annotidmax = 48 nlabels = 48 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgz Mapping Segmentation fault

----Same thing occurs for the right hemi

On Wed, Jun 22, 2022 at 11:42 AM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,

Do you mean the issue that ‘mri_label2vol –fill-ribbon’ crashes? Can you re-run and provide your mris_label2annot and mri_label2vol command line and output?

I’m not sure I will be able to offer work around, but I would like to understand the problem better for future development.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Tuesday, June 21, 2022 5:04 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

It seems that this did not solve the issue. Are there any other reasons why this would occur?

Ben

On Fri, Jun 17, 2022 at 2:59 PM Benjamin Deck <bdeck8317@gmail.commailto:bdeck8317@gmail.com> wrote: Hi Yujing,

Thank you. I will give it a try! Can documentation be updated?

Ben

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On Fri, Jun 17, 2022 at 2:56 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,

Just wanted to update you on mris_label2annot command line options.

If ‘--no-unknown’ is used with mris_label2annot, ‘—offset 1’ should also be specified.

Yujing

From: Huang, Yujing Sent: Thursday, June 16, 2022 1:59 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: RE: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

Hi Ben,

I’m learning it myself too.

I played it a little more. I see the mismatch can happen if you skip a number in you LUT.

Also, if you have ‘0 Unknown 0 0 0 0’ in your LUT, I’m not sure you should use ‘--no-unknown’ for mris_label2annot. It will cause your annotation off by one.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Thursday, June 16, 2022 10:58 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

Thanks for taking a look. What do you mean by mismatch?

The LUT was used to make the annot file. What would generate this mismatch?

Here is the output from my mris_label2annot call:

mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --hemi lh Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 105 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 1 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_10_ROIs_1_lh_native.label 2 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_11_ROIs_1_lh_native.label 3 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_1_lh_native.label 4 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_2_lh_native.label 5 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_1_lh_native.label 6 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_2_lh_native.label 7 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_3_lh_native.label 8 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_4_lh_native.label 9 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_5_lh_native.label 10 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_1_lh_native.label 11 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_2_lh_native.label 12 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_3_lh_native.label 13 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_4_lh_native.label 14 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_5_lh_native.label 15 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_15_ROIs_1_lh_native.label 16 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_1_lh_native.label 17 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_2_lh_native.label 18 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_1_lh_native.label 19 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_2_lh_native.label 20 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_3_lh_native.label 21 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_4_lh_native.label 22 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_1_lh_native.label 23 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_2_lh_native.label 24 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_3_lh_native.label 25 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_4_lh_native.label 26 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_5_lh_native.label 27 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_19_ROIs_1_lh_native.label 28 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_1_lh_native.label 29 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_2_lh_native.label 30 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_1_lh_native.label 31 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_2_lh_native.label 32 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_3_lh_native.label 33 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_4_ROIs_1_lh_native.label 34 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_1_lh_native.label 35 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_2_lh_native.label 36 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_3_lh_native.label 37 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_4_lh_native.label 38 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_1_lh_native.label 39 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_2_lh_native.label 40 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_3_lh_native.label 41 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_1_lh_native.label 42 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_2_lh_native.label 43 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_1_lh_native.label 44 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_2_lh_native.label 45 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_3_lh_native.label 46 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_4_lh_native.label 47 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_5_lh_native.label 48 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_1_lh_native.label 49 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_2_lh_native.label 50 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_3_lh_native.label

7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --hemi lh sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 50 LabelThresh 0 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig 0 1336330 Net_10_ROIs_1_lh_native 1 1639705 Net_11_ROIs_1_lh_native 2 2647065 Net_12_ROIs_1_lh_native 3 11829830 Net_12_ROIs_2_lh_native 4 25700 Net_13_ROIs_1_lh_native 5 16399044 Net_13_ROIs_2_lh_native 6 6500 Net_13_ROIs_3_lh_native 7 3294840 Net_13_ROIs_4_lh_native 8 660700 Net_13_ROIs_5_lh_native 9 6558940 Net_14_ROIs_1_lh_native 10 7874740 Net_14_ROIs_2_lh_native 11 14465658 Net_14_ROIs_3_lh_native 12 9180300 Net_14_ROIs_4_lh_native 13 12300 Net_14_ROIs_5_lh_native 14 9182740 Net_15_ROIs_1_lh_native 15 3296035 Net_16_ROIs_1_lh_native 16 9211105 Net_16_ROIs_2_lh_native 17 4924360 Net_17_ROIs_1_lh_native 18 3302560 Net_17_ROIs_2_lh_native 19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native 21 13777468 Net_18_ROIs_1_lh_native 22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native 24 3294765 Net_18_ROIs_4_lh_native 25 14443610 Net_18_ROIs_5_lh_native 26 10511400 Net_19_ROIs_1_lh_native 27 8323072 Net_2_ROIs_1_lh_native 28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native 30 1316060 Net_3_ROIs_2_lh_native 31 14464220 Net_3_ROIs_3_lh_native 32 8323072 Net_4_ROIs_1_lh_native 33 7874740 Net_5_ROIs_1_lh_native 34 9180300 Net_5_ROIs_2_lh_native 35 8860211 Net_5_ROIs_3_lh_native 36 9182740 Net_5_ROIs_4_lh_native 37 3296035 Net_6_ROIs_1_lh_native 38 9211105 Net_6_ROIs_2_lh_native 39 4924360 Net_6_ROIs_3_lh_native 40 3302560 Net_7_ROIs_1_lh_native 41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native 45 3302620 Net_8_ROIs_4_lh_native 46 10811612 Net_8_ROIs_5_lh_native 47 2637020 Net_9_ROIs_1_lh_native 48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot

Thanks,

Ben

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On Tue, Jun 14, 2022 at 1:33 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,

I was able to reproduce the core dump. In my case, it was because a mismatch of color scheme between input annotation file and the color table loaded with the surface.

I suspect it might be the same issue for you too. But I’m not sure what the right action is to work around this.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Friday, June 10, 2022 11:47 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi there,

Having issues with the following command:

mri_label2vol --annot lh.yeo_2011.annot --temp /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz --hemi lh --fill-ribbon --identity --subject sub-DAEK --o lh.sub-DAEK_annot_nat.nii.gz

produces the following error:

Number of labels: 0 Annot File: lh.yeo_2011.annot Template Volume: /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz Outut Volume: lh.sub-DAEK_annot_nat.nii.gz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: sub-DAEK Hemi: lh UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects 7.2.0 Template RAS-to-Vox: -------- -1.25000 -0.00000 -0.00000 160.00000; -0.00000 -0.00000 -1.25000 160.00000; -0.00000 1.25000 -0.00000 160.00000; -0.00000 -0.00000 -0.00000 1.00000; Template Voxel Volume: 0.512 nHits Thresh: 0 Using Identity Matrix RegMat: -------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Label RAS-to-Vox: -------- -1.25000 0.00000 0.00000 160.00000; 0.00000 0.00000 -1.25000 160.00000; 0.00000 1.25000 0.00000 160.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.white nvertices = 253237 Reading thickness /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.thickness Loading annotations from lh.yeo_2011.annot annotidmax = 48 nlabels = 48 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgz Mapping Segmentation fault

But when I run the same command without fill-ribbon the process runs to completion.

Not sure if this is a memory issue or something else.

Ben

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University

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-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1pg-D_wLryyZksJTKvQ2XCj2jB5SkB2H8DVHgj5FtQzPyNkniuHdTaL_IBFsxabyNQVwyDAGRDb0cGEIzTIwtcuvIjwV3Lg7QiLDyCU74wL7e7OWYfCCCREmXi9pTrSNypqR7dIGxdS9SqZWfBT2kNZZz3MP8T3iMaDPJB9tUGA0ftI51Y1MpTzJb0BuB7LpTw9riLUlNPvZd3ibg1m7sC629TtuUgdOT-UbH-LxXKgxPhoGJTq0JLzVzIVxqiHbwMlHBsuO84niKNg6mU818Tct_f3UyRX5FTrDYdFHzIsp8PP-5erbf9ISg_MOJtcBAuHtG9F7ocoXiqQITXSSQuw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1ewws5jb1hRDkswPgWMqJP5exouHEKg_qKAlpTyoWlL_21LVGF-OMt6D7Slbg57sQbZwXOVLoDnC9YmdlJJzCPz_HQflF5OSUSoOzRFqBb6S3Zj7jBeo3gp2dpeZTH5IAbvwMwJpAhQONN1708QcTAGvm0HQozK-hXCPgp3gdbe5lVhSGPdR8e1sEZJXq-rZdgdTLIf1a_-e1YvYd5r2ev1HhSuWmyQ5RsQA7Bcb_Rh2TEkdyOmIr0twh52ig6Lrx-_i0r-cciGHcHqmJL_nfrTjOePOVj-htPLFiL1A6BFbEZOUR5-kiUNSZMT9PrStO3fWQUbb7X1WIRA8SBCJQXg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1ewws5jb1hRDkswPgWMqJP5exouHEKg_qKAlpTyoWlL_21LVGF-OMt6D7Slbg57sQbZwXOVLoDnC9YmdlJJzCPz_HQflF5OSUSoOzRFqBb6S3Zj7jBeo3gp2dpeZTH5IAbvwMwJpAhQONN1708QcTAGvm0HQozK-hXCPgp3gdbe5lVhSGPdR8e1sEZJXq-rZdgdTLIf1a_-e1YvYd5r2ev1HhSuWmyQ5RsQA7Bcb_Rh2TEkdyOmIr0twh52ig6Lrx-_i0r-cciGHcHqmJL_nfrTjOePOVj-htPLFiL1A6BFbEZOUR5-kiUNSZMT9PrStO3fWQUbb7X1WIRA8SBCJQXg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University

I am confused about ‘—no-unknown –offset 0’. Your output doesn’t seem agree with the codes. If your label starts at 1, I think it should be ‘—offset 1’ instead of 0. Can you double check your LUT?

I see duplicates in second column of these lines: (second column is calculated from RGB values.)

19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native

22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native

28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native

41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native

48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Benjamin Deck Sent: Thursday, June 23, 2022 9:36 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

I am not seeing any duplicates--highlighting wasn't rendered on my end.

my LUT:

0 Unknown 0 0 0 0 1 Net_10_ROIs_1_lh_native 255 255 255 0 2 Net_11_ROIs_1_lh_native 25 5 25 0 3 Net_12_ROIs_1_lh_native 25 100 40 0 4 Net_12_ROIs_2_lh_native 70 130 180 0 5 Net_13_ROIs_1_lh_native 100 100 0 0 6 Net_13_ROIs_2_lh_native 196 58 250 0

which is why I gave the --offset flag as 0 for --no-unknown

I did notice that the labels is incorrect. So for some reason, it seems to be missing two labels that exist in the annotation. That is strange.

Ben

On Thu, Jun 23, 2022 at 8:55 AM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: How does your LUT look like? What is your first line?

For left hemi, your loaded 50 label files to mris_label2annot, but mri_label2vol only reported 48 labels. It looks like you have duplicated RGB in your LUT. I have identified some. See highlighted in red. The duplicated RGB entries can cause problems.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Wednesday, June 22, 2022 2:24 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

Sure thing.

Commands:

mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt

Output: Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 105 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 1 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_10_ROIs_1_lh_native.label 2 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_11_ROIs_1_lh_native.label 3 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_1_lh_native.label 4 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_2_lh_native.label 5 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_1_lh_native.label 6 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_2_lh_native.label 7 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_3_lh_native.label 8 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_4_lh_native.label 9 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_5_lh_native.label 10 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_1_lh_native.label 11 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_2_lh_native.label 12 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_3_lh_native.label 13 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_4_lh_native.label 14 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_5_lh_native.label 15 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_15_ROIs_1_lh_native.label 16 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_1_lh_native.label 17 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_2_lh_native.label 18 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_1_lh_native.label 19 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_2_lh_native.label 20 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_3_lh_native.label 21 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_4_lh_native.label 22 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_1_lh_native.label 23 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_2_lh_native.label 24 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_3_lh_native.label 25 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_4_lh_native.label 26 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_5_lh_native.label 27 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_19_ROIs_1_lh_native.label 28 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_1_lh_native.label 29 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_2_lh_native.label 30 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_1_lh_native.label 31 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_2_lh_native.label 32 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_3_lh_native.label 33 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_4_ROIs_1_lh_native.label 34 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_1_lh_native.label 35 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_2_lh_native.label 36 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_3_lh_native.label 37 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_4_lh_native.label 38 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_1_lh_native.label 39 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_2_lh_native.label 40 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_3_lh_native.label 41 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_1_lh_native.label 42 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_2_lh_native.label 43 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_1_lh_native.label 44 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_2_lh_native.label 45 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_3_lh_native.label 46 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_4_lh_native.label 47 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_5_lh_native.label 48 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_1_lh_native.label 49 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_2_lh_native.label 50 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_3_lh_native.label

7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 50 LabelThresh 1 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig 0 16777215 Net_10_ROIs_1_lh_native 1 1639705 Net_11_ROIs_1_lh_native 2 2647065 Net_12_ROIs_1_lh_native 3 11829830 Net_12_ROIs_2_lh_native 4 25700 Net_13_ROIs_1_lh_native 5 16399044 Net_13_ROIs_2_lh_native 6 6500 Net_13_ROIs_3_lh_native 7 3294840 Net_13_ROIs_4_lh_native 8 660700 Net_13_ROIs_5_lh_native 9 6558940 Net_14_ROIs_1_lh_native 10 7874740 Net_14_ROIs_2_lh_native 11 14465658 Net_14_ROIs_3_lh_native 12 9180300 Net_14_ROIs_4_lh_native 13 12300 Net_14_ROIs_5_lh_native 14 9182740 Net_15_ROIs_1_lh_native 15 3296035 Net_16_ROIs_1_lh_native 16 9211105 Net_16_ROIs_2_lh_native 17 4924360 Net_17_ROIs_1_lh_native 18 3302560 Net_17_ROIs_2_lh_native 19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native 21 13777468 Net_18_ROIs_1_lh_native 22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native 24 3294765 Net_18_ROIs_4_lh_native 25 14443610 Net_18_ROIs_5_lh_native 26 10511400 Net_19_ROIs_1_lh_native 27 8323072 Net_2_ROIs_1_lh_native 28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native 30 1316060 Net_3_ROIs_2_lh_native 31 14464220 Net_3_ROIs_3_lh_native 32 8323072 Net_4_ROIs_1_lh_native 33 7874740 Net_5_ROIs_1_lh_native 34 9180300 Net_5_ROIs_2_lh_native 35 8860211 Net_5_ROIs_3_lh_native 36 9182740 Net_5_ROIs_4_lh_native 37 3296035 Net_6_ROIs_1_lh_native 38 9211105 Net_6_ROIs_2_lh_native 39 4924360 Net_6_ROIs_3_lh_native 40 3302560 Net_7_ROIs_1_lh_native 41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native 45 3302620 Net_8_ROIs_4_lh_native 46 10811612 Net_8_ROIs_5_lh_native 47 2637020 Net_9_ROIs_1_lh_native 48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot

command: mris_label2annot --s sub-DAEK --hemi rh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt

output: Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 105 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 51 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_10_ROIs_1_rh_native.label 52 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_11_ROIs_1_rh_native.label 53 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_12_ROIs_1_rh_native.label 54 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_12_ROIs_2_rh_native.label 55 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_1_rh_native.label 56 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_2_rh_native.label 57 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_3_rh_native.label 58 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_4_rh_native.label 59 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_1_rh_native.label 60 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_2_rh_native.label 61 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_3_rh_native.label 62 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_4_rh_native.label 63 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_5_rh_native.label 64 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_15_ROIs_1_rh_native.label 65 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_1_rh_native.label 66 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_2_rh_native.label 67 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_3_rh_native.label 68 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_1_rh_native.label 69 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_2_rh_native.label 70 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_3_rh_native.label 71 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_4_rh_native.label 72 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_1_rh_native.label 73 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_2_rh_native.label 74 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_3_rh_native.label 75 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_4_rh_native.label 76 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_19_ROIs_1_rh_native.label 77 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_2_ROIs_1_rh_native.label 78 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_2_ROIs_2_rh_native.label 79 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_1_rh_native.label 80 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_2_rh_native.label 81 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_3_rh_native.label 82 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_4_ROIs_1_rh_native.label 83 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_1_rh_native.label 84 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_2_rh_native.label 85 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_3_rh_native.label 86 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_4_rh_native.label 87 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_1_rh_native.label 88 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_2_rh_native.label 89 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_3_rh_native.label 90 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_1_rh_native.label 91 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_2_rh_native.label 92 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_3_rh_native.label 93 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_1_rh_native.label 94 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_2_rh_native.label 95 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_3_rh_native.label 96 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_4_rh_native.label 97 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_5_rh_native.label 98 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_6_rh_native.label 99 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_1_rh_native.label 100 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_2_rh_native.label 101 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_3_rh_native.label 102 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_4_rh_native.label 103 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_5_rh_native.label 104 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_6_rh_native.label

7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --hemi rh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi rh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 54 LabelThresh 1 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/rh.orig 0 1316060 Net_10_ROIs_1_rh_native 1 14464220 Net_11_ROIs_1_rh_native 2 14423100 Net_12_ROIs_1_rh_native 3 11832480 Net_12_ROIs_2_rh_native 4 9180240 Net_13_ROIs_1_rh_native 5 8204875 Net_13_ROIs_2_rh_native 6 10542100 Net_13_ROIs_3_rh_native 7 9231380 Net_13_ROIs_4_rh_native 8 9221140 Net_14_ROIs_1_rh_native 9 14474380 Net_14_ROIs_2_rh_native 10 2763429 Net_14_ROIs_3_rh_native 11 1351760 Net_14_ROIs_4_rh_native 12 15736992 Net_14_ROIs_5_rh_native 13 6553700 Net_15_ROIs_1_rh_native 14 11146310 Net_16_ROIs_1_rh_native 15 13145750 Net_16_ROIs_2_rh_native 16 3311482 Net_16_ROIs_3_rh_native 17 2146304 Net_17_ROIs_1_rh_native 18 5935475 Net_17_ROIs_2_rh_native 19 681085 Net_17_ROIs_3_rh_native 20 23060 Net_17_ROIs_4_rh_native 21 3957760 Net_18_ROIs_1_rh_native 22 3311482 Net_18_ROIs_2_rh_native 23 1321040 Net_18_ROIs_3_rh_native 24 3276922 Net_18_ROIs_4_rh_native 25 6588260 Net_19_ROIs_1_rh_native 26 3957760 Net_2_ROIs_1_rh_native 27 50372 Net_2_ROIs_2_rh_native 28 2671812 Net_3_ROIs_1_rh_native 29 3957956 Net_3_ROIs_2_rh_native 30 6564036 Net_3_ROIs_3_rh_native 31 3945156 Net_4_ROIs_1_rh_native 32 13127690 Net_5_ROIs_1_rh_native 33 6604880 Net_5_ROIs_2_rh_native 34 2647140 Net_5_ROIs_3_rh_native 35 3937480 Net_5_ROIs_4_rh_native 36 665610 Net_6_ROIs_1_rh_native 37 50372 Net_6_ROIs_2_rh_native 38 706590 Net_6_ROIs_3_rh_native 39 5923840 Net_7_ROIs_1_rh_native 40 6579200 Net_7_ROIs_2_rh_native 41 32768 Net_7_ROIs_3_rh_native 42 25600 Net_8_ROIs_1_rh_native 43 13117500 Net_8_ROIs_2_rh_native 44 6574090 Net_8_ROIs_3_rh_native 45 51200 Net_8_ROIs_4_rh_native 46 8320 Net_8_ROIs_5_rh_native 47 25750 Net_8_ROIs_6_rh_native 48 1336330 Net_9_ROIs_1_rh_native 49 25740 Net_9_ROIs_2_rh_native 50 3983360 Net_9_ROIs_3_rh_native 51 7895160 Net_9_ROIs_4_rh_native 52 6553720 Net_9_ROIs_5_rh_native 53 8312 Net_9_ROIs_6_rh_native Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/rh.yeo2011.annot

---Annotations look fine.

Command: mri_label2vol --o lh.yeo2011_in_nat.mgz --annot ../lh.yeo2011.annot --identity --fill-ribbon --subject sub-DAEK --h emi lh

Output: Number of labels: 0 Annot File: ../lh.yeo2011.annot Template Volume: (null) Outut Volume: lh.yeo2011_in_nat.mgz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: sub-DAEK Hemi: lh UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects 7.2.0 INFO: loading surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.white nvertices = 253237 Reading thickness /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.thickness Loading annotations from ../lh.yeo2011.annot annotidmax = 48 nlabels = 48 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgz Mapping Segmentation fault

----Same thing occurs for the right hemi

On Wed, Jun 22, 2022 at 11:42 AM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,

Do you mean the issue that ‘mri_label2vol –fill-ribbon’ crashes? Can you re-run and provide your mris_label2annot and mri_label2vol command line and output?

I’m not sure I will be able to offer work around, but I would like to understand the problem better for future development.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Tuesday, June 21, 2022 5:04 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

It seems that this did not solve the issue. Are there any other reasons why this would occur?

Ben

On Fri, Jun 17, 2022 at 2:59 PM Benjamin Deck <bdeck8317@gmail.commailto:bdeck8317@gmail.com> wrote: Hi Yujing,

Thank you. I will give it a try! Can documentation be updated?

Ben

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On Fri, Jun 17, 2022 at 2:56 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,

Just wanted to update you on mris_label2annot command line options.

If ‘--no-unknown’ is used with mris_label2annot, ‘—offset 1’ should also be specified.

Yujing

From: Huang, Yujing Sent: Thursday, June 16, 2022 1:59 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: RE: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

Hi Ben,

I’m learning it myself too.

I played it a little more. I see the mismatch can happen if you skip a number in you LUT.

Also, if you have ‘0 Unknown 0 0 0 0’ in your LUT, I’m not sure you should use ‘--no-unknown’ for mris_label2annot. It will cause your annotation off by one.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Thursday, June 16, 2022 10:58 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

Thanks for taking a look. What do you mean by mismatch?

The LUT was used to make the annot file. What would generate this mismatch?

Here is the output from my mris_label2annot call:

mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --hemi lh Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 105 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 1 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_10_ROIs_1_lh_native.label 2 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_11_ROIs_1_lh_native.label 3 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_1_lh_native.label 4 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_2_lh_native.label 5 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_1_lh_native.label 6 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_2_lh_native.label 7 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_3_lh_native.label 8 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_4_lh_native.label 9 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_5_lh_native.label 10 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_1_lh_native.label 11 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_2_lh_native.label 12 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_3_lh_native.label 13 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_4_lh_native.label 14 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_5_lh_native.label 15 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_15_ROIs_1_lh_native.label 16 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_1_lh_native.label 17 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_2_lh_native.label 18 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_1_lh_native.label 19 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_2_lh_native.label 20 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_3_lh_native.label 21 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_4_lh_native.label 22 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_1_lh_native.label 23 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_2_lh_native.label 24 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_3_lh_native.label 25 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_4_lh_native.label 26 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_5_lh_native.label 27 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_19_ROIs_1_lh_native.label 28 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_1_lh_native.label 29 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_2_lh_native.label 30 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_1_lh_native.label 31 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_2_lh_native.label 32 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_3_lh_native.label 33 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_4_ROIs_1_lh_native.label 34 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_1_lh_native.label 35 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_2_lh_native.label 36 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_3_lh_native.label 37 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_4_lh_native.label 38 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_1_lh_native.label 39 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_2_lh_native.label 40 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_3_lh_native.label 41 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_1_lh_native.label 42 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_2_lh_native.label 43 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_1_lh_native.label 44 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_2_lh_native.label 45 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_3_lh_native.label 46 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_4_lh_native.label 47 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_5_lh_native.label 48 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_1_lh_native.label 49 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_2_lh_native.label 50 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_3_lh_native.label

7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --hemi lh sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 50 LabelThresh 0 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig 0 1336330 Net_10_ROIs_1_lh_native 1 1639705 Net_11_ROIs_1_lh_native 2 2647065 Net_12_ROIs_1_lh_native 3 11829830 Net_12_ROIs_2_lh_native 4 25700 Net_13_ROIs_1_lh_native 5 16399044 Net_13_ROIs_2_lh_native 6 6500 Net_13_ROIs_3_lh_native 7 3294840 Net_13_ROIs_4_lh_native 8 660700 Net_13_ROIs_5_lh_native 9 6558940 Net_14_ROIs_1_lh_native 10 7874740 Net_14_ROIs_2_lh_native 11 14465658 Net_14_ROIs_3_lh_native 12 9180300 Net_14_ROIs_4_lh_native 13 12300 Net_14_ROIs_5_lh_native 14 9182740 Net_15_ROIs_1_lh_native 15 3296035 Net_16_ROIs_1_lh_native 16 9211105 Net_16_ROIs_2_lh_native 17 4924360 Net_17_ROIs_1_lh_native 18 3302560 Net_17_ROIs_2_lh_native 19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native 21 13777468 Net_18_ROIs_1_lh_native 22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native 24 3294765 Net_18_ROIs_4_lh_native 25 14443610 Net_18_ROIs_5_lh_native 26 10511400 Net_19_ROIs_1_lh_native 27 8323072 Net_2_ROIs_1_lh_native 28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native 30 1316060 Net_3_ROIs_2_lh_native 31 14464220 Net_3_ROIs_3_lh_native 32 8323072 Net_4_ROIs_1_lh_native 33 7874740 Net_5_ROIs_1_lh_native 34 9180300 Net_5_ROIs_2_lh_native 35 8860211 Net_5_ROIs_3_lh_native 36 9182740 Net_5_ROIs_4_lh_native 37 3296035 Net_6_ROIs_1_lh_native 38 9211105 Net_6_ROIs_2_lh_native 39 4924360 Net_6_ROIs_3_lh_native 40 3302560 Net_7_ROIs_1_lh_native 41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native 45 3302620 Net_8_ROIs_4_lh_native 46 10811612 Net_8_ROIs_5_lh_native 47 2637020 Net_9_ROIs_1_lh_native 48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot

Thanks,

Ben

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On Tue, Jun 14, 2022 at 1:33 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,

I was able to reproduce the core dump. In my case, it was because a mismatch of color scheme between input annotation file and the color table loaded with the surface.

I suspect it might be the same issue for you too. But I’m not sure what the right action is to work around this.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Friday, June 10, 2022 11:47 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi there,

Having issues with the following command:

mri_label2vol --annot lh.yeo_2011.annot --temp /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz --hemi lh --fill-ribbon --identity --subject sub-DAEK --o lh.sub-DAEK_annot_nat.nii.gz

produces the following error:

Number of labels: 0 Annot File: lh.yeo_2011.annot Template Volume: /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz Outut Volume: lh.sub-DAEK_annot_nat.nii.gz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: sub-DAEK Hemi: lh UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects 7.2.0 Template RAS-to-Vox: -------- -1.25000 -0.00000 -0.00000 160.00000; -0.00000 -0.00000 -1.25000 160.00000; -0.00000 1.25000 -0.00000 160.00000; -0.00000 -0.00000 -0.00000 1.00000; Template Voxel Volume: 0.512 nHits Thresh: 0 Using Identity Matrix RegMat: -------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Label RAS-to-Vox: -------- -1.25000 0.00000 0.00000 160.00000; 0.00000 0.00000 -1.25000 160.00000; 0.00000 1.25000 0.00000 160.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.white nvertices = 253237 Reading thickness /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.thickness Loading annotations from lh.yeo_2011.annot annotidmax = 48 nlabels = 48 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgz Mapping Segmentation fault

But when I run the same command without fill-ribbon the process runs to completion.

Not sure if this is a memory issue or something else.

Ben

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University

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-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University

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For the duplicates, 19 is same as 41, 20 is same as 42, …

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Benjamin Deck Sent: Thursday, June 23, 2022 10:27 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

Thanks for your continued support on this issue.

Addressing your first question.

If I use --offset 1 then the get the following:

cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --offset 1 sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 50 LabelThresh 1 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig 1 1639705 Net_11_ROIs_1_lh_native 2 2647065 Net_12_ROIs_1_lh_native 3 11829830 Net_12_ROIs_2_lh_native 4 25700 Net_13_ROIs_1_lh_native 5 16399044 Net_13_ROIs_2_lh_native 6 6500 Net_13_ROIs_3_lh_native 7 3294840 Net_13_ROIs_4_lh_native 8 660700 Net_13_ROIs_5_lh_native 9 6558940 Net_14_ROIs_1_lh_native 10 7874740 Net_14_ROIs_2_lh_native 11 14465658 Net_14_ROIs_3_lh_native 12 9180300 Net_14_ROIs_4_lh_native 13 12300 Net_14_ROIs_5_lh_native 14 9182740 Net_15_ROIs_1_lh_native 15 3296035 Net_16_ROIs_1_lh_native 16 9211105 Net_16_ROIs_2_lh_native 17 4924360 Net_17_ROIs_1_lh_native 18 3302560 Net_17_ROIs_2_lh_native 19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native 21 13777468 Net_18_ROIs_1_lh_native 22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native 24 3294765 Net_18_ROIs_4_lh_native 25 14443610 Net_18_ROIs_5_lh_native 26 10511400 Net_19_ROIs_1_lh_native 27 8323072 Net_2_ROIs_1_lh_native 28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native 30 1316060 Net_3_ROIs_2_lh_native 31 14464220 Net_3_ROIs_3_lh_native 32 8323072 Net_4_ROIs_1_lh_native 33 7874740 Net_5_ROIs_1_lh_native 34 9180300 Net_5_ROIs_2_lh_native 35 8860211 Net_5_ROIs_3_lh_native 36 9182740 Net_5_ROIs_4_lh_native 37 3296035 Net_6_ROIs_1_lh_native 38 9211105 Net_6_ROIs_2_lh_native 39 4924360 Net_6_ROIs_3_lh_native 40 3302560 Net_7_ROIs_1_lh_native 41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native 45 3302620 Net_8_ROIs_4_lh_native 46 10811612 Net_8_ROIs_5_lh_native 47 2637020 Net_9_ROIs_1_lh_native 48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native 50 791413 cluster50 Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot

Where cluster50 is some nondescript cluster and it ignores my network 10 which should be the first entry.

To address your second question about duplicates.

19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native

While these may look almost like duplicates they are different rois within the same larger network. This separation is important for what I am doing so I need to keep the ROIs separate from one another but they are a part of the same larger network. However, Freesurfer doesn't know that they are.

On Thu, Jun 23, 2022 at 10:17 AM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: I am confused about ‘—no-unknown –offset 0’. Your output doesn’t seem agree with the codes. If your label starts at 1, I think it should be ‘—offset 1’ instead of 0. Can you double check your LUT?

I see duplicates in second column of these lines: (second column is calculated from RGB values.)

19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native

22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native

28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native

41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native

48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Thursday, June 23, 2022 9:36 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

I am not seeing any duplicates--highlighting wasn't rendered on my end.

my LUT:

0 Unknown 0 0 0 0 1 Net_10_ROIs_1_lh_native 255 255 255 0 2 Net_11_ROIs_1_lh_native 25 5 25 0 3 Net_12_ROIs_1_lh_native 25 100 40 0 4 Net_12_ROIs_2_lh_native 70 130 180 0 5 Net_13_ROIs_1_lh_native 100 100 0 0 6 Net_13_ROIs_2_lh_native 196 58 250 0

which is why I gave the --offset flag as 0 for --no-unknown

I did notice that the labels is incorrect. So for some reason, it seems to be missing two labels that exist in the annotation. That is strange.

Ben

On Thu, Jun 23, 2022 at 8:55 AM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: How does your LUT look like? What is your first line?

For left hemi, your loaded 50 label files to mris_label2annot, but mri_label2vol only reported 48 labels. It looks like you have duplicated RGB in your LUT. I have identified some. See highlighted in red. The duplicated RGB entries can cause problems.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Wednesday, June 22, 2022 2:24 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

Sure thing.

Commands:

mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt

Output: Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 105 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 1 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_10_ROIs_1_lh_native.label 2 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_11_ROIs_1_lh_native.label 3 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_1_lh_native.label 4 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_2_lh_native.label 5 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_1_lh_native.label 6 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_2_lh_native.label 7 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_3_lh_native.label 8 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_4_lh_native.label 9 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_5_lh_native.label 10 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_1_lh_native.label 11 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_2_lh_native.label 12 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_3_lh_native.label 13 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_4_lh_native.label 14 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_5_lh_native.label 15 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_15_ROIs_1_lh_native.label 16 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_1_lh_native.label 17 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_2_lh_native.label 18 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_1_lh_native.label 19 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_2_lh_native.label 20 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_3_lh_native.label 21 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_4_lh_native.label 22 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_1_lh_native.label 23 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_2_lh_native.label 24 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_3_lh_native.label 25 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_4_lh_native.label 26 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_5_lh_native.label 27 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_19_ROIs_1_lh_native.label 28 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_1_lh_native.label 29 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_2_lh_native.label 30 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_1_lh_native.label 31 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_2_lh_native.label 32 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_3_lh_native.label 33 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_4_ROIs_1_lh_native.label 34 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_1_lh_native.label 35 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_2_lh_native.label 36 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_3_lh_native.label 37 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_4_lh_native.label 38 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_1_lh_native.label 39 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_2_lh_native.label 40 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_3_lh_native.label 41 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_1_lh_native.label 42 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_2_lh_native.label 43 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_1_lh_native.label 44 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_2_lh_native.label 45 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_3_lh_native.label 46 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_4_lh_native.label 47 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_5_lh_native.label 48 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_1_lh_native.label 49 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_2_lh_native.label 50 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_3_lh_native.label

7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 50 LabelThresh 1 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig 0 16777215 Net_10_ROIs_1_lh_native 1 1639705 Net_11_ROIs_1_lh_native 2 2647065 Net_12_ROIs_1_lh_native 3 11829830 Net_12_ROIs_2_lh_native 4 25700 Net_13_ROIs_1_lh_native 5 16399044 Net_13_ROIs_2_lh_native 6 6500 Net_13_ROIs_3_lh_native 7 3294840 Net_13_ROIs_4_lh_native 8 660700 Net_13_ROIs_5_lh_native 9 6558940 Net_14_ROIs_1_lh_native 10 7874740 Net_14_ROIs_2_lh_native 11 14465658 Net_14_ROIs_3_lh_native 12 9180300 Net_14_ROIs_4_lh_native 13 12300 Net_14_ROIs_5_lh_native 14 9182740 Net_15_ROIs_1_lh_native 15 3296035 Net_16_ROIs_1_lh_native 16 9211105 Net_16_ROIs_2_lh_native 17 4924360 Net_17_ROIs_1_lh_native 18 3302560 Net_17_ROIs_2_lh_native 19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native 21 13777468 Net_18_ROIs_1_lh_native 22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native 24 3294765 Net_18_ROIs_4_lh_native 25 14443610 Net_18_ROIs_5_lh_native 26 10511400 Net_19_ROIs_1_lh_native 27 8323072 Net_2_ROIs_1_lh_native 28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native 30 1316060 Net_3_ROIs_2_lh_native 31 14464220 Net_3_ROIs_3_lh_native 32 8323072 Net_4_ROIs_1_lh_native 33 7874740 Net_5_ROIs_1_lh_native 34 9180300 Net_5_ROIs_2_lh_native 35 8860211 Net_5_ROIs_3_lh_native 36 9182740 Net_5_ROIs_4_lh_native 37 3296035 Net_6_ROIs_1_lh_native 38 9211105 Net_6_ROIs_2_lh_native 39 4924360 Net_6_ROIs_3_lh_native 40 3302560 Net_7_ROIs_1_lh_native 41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native 45 3302620 Net_8_ROIs_4_lh_native 46 10811612 Net_8_ROIs_5_lh_native 47 2637020 Net_9_ROIs_1_lh_native 48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot

command: mris_label2annot --s sub-DAEK --hemi rh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt

output: Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 105 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 51 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_10_ROIs_1_rh_native.label 52 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_11_ROIs_1_rh_native.label 53 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_12_ROIs_1_rh_native.label 54 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_12_ROIs_2_rh_native.label 55 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_1_rh_native.label 56 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_2_rh_native.label 57 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_3_rh_native.label 58 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_4_rh_native.label 59 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_1_rh_native.label 60 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_2_rh_native.label 61 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_3_rh_native.label 62 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_4_rh_native.label 63 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_5_rh_native.label 64 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_15_ROIs_1_rh_native.label 65 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_1_rh_native.label 66 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_2_rh_native.label 67 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_3_rh_native.label 68 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_1_rh_native.label 69 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_2_rh_native.label 70 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_3_rh_native.label 71 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_4_rh_native.label 72 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_1_rh_native.label 73 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_2_rh_native.label 74 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_3_rh_native.label 75 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_4_rh_native.label 76 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_19_ROIs_1_rh_native.label 77 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_2_ROIs_1_rh_native.label 78 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_2_ROIs_2_rh_native.label 79 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_1_rh_native.label 80 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_2_rh_native.label 81 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_3_rh_native.label 82 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_4_ROIs_1_rh_native.label 83 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_1_rh_native.label 84 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_2_rh_native.label 85 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_3_rh_native.label 86 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_4_rh_native.label 87 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_1_rh_native.label 88 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_2_rh_native.label 89 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_3_rh_native.label 90 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_1_rh_native.label 91 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_2_rh_native.label 92 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_3_rh_native.label 93 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_1_rh_native.label 94 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_2_rh_native.label 95 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_3_rh_native.label 96 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_4_rh_native.label 97 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_5_rh_native.label 98 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_6_rh_native.label 99 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_1_rh_native.label 100 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_2_rh_native.label 101 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_3_rh_native.label 102 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_4_rh_native.label 103 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_5_rh_native.label 104 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_6_rh_native.label

7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --hemi rh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi rh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 54 LabelThresh 1 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/rh.orig 0 1316060 Net_10_ROIs_1_rh_native 1 14464220 Net_11_ROIs_1_rh_native 2 14423100 Net_12_ROIs_1_rh_native 3 11832480 Net_12_ROIs_2_rh_native 4 9180240 Net_13_ROIs_1_rh_native 5 8204875 Net_13_ROIs_2_rh_native 6 10542100 Net_13_ROIs_3_rh_native 7 9231380 Net_13_ROIs_4_rh_native 8 9221140 Net_14_ROIs_1_rh_native 9 14474380 Net_14_ROIs_2_rh_native 10 2763429 Net_14_ROIs_3_rh_native 11 1351760 Net_14_ROIs_4_rh_native 12 15736992 Net_14_ROIs_5_rh_native 13 6553700 Net_15_ROIs_1_rh_native 14 11146310 Net_16_ROIs_1_rh_native 15 13145750 Net_16_ROIs_2_rh_native 16 3311482 Net_16_ROIs_3_rh_native 17 2146304 Net_17_ROIs_1_rh_native 18 5935475 Net_17_ROIs_2_rh_native 19 681085 Net_17_ROIs_3_rh_native 20 23060 Net_17_ROIs_4_rh_native 21 3957760 Net_18_ROIs_1_rh_native 22 3311482 Net_18_ROIs_2_rh_native 23 1321040 Net_18_ROIs_3_rh_native 24 3276922 Net_18_ROIs_4_rh_native 25 6588260 Net_19_ROIs_1_rh_native 26 3957760 Net_2_ROIs_1_rh_native 27 50372 Net_2_ROIs_2_rh_native 28 2671812 Net_3_ROIs_1_rh_native 29 3957956 Net_3_ROIs_2_rh_native 30 6564036 Net_3_ROIs_3_rh_native 31 3945156 Net_4_ROIs_1_rh_native 32 13127690 Net_5_ROIs_1_rh_native 33 6604880 Net_5_ROIs_2_rh_native 34 2647140 Net_5_ROIs_3_rh_native 35 3937480 Net_5_ROIs_4_rh_native 36 665610 Net_6_ROIs_1_rh_native 37 50372 Net_6_ROIs_2_rh_native 38 706590 Net_6_ROIs_3_rh_native 39 5923840 Net_7_ROIs_1_rh_native 40 6579200 Net_7_ROIs_2_rh_native 41 32768 Net_7_ROIs_3_rh_native 42 25600 Net_8_ROIs_1_rh_native 43 13117500 Net_8_ROIs_2_rh_native 44 6574090 Net_8_ROIs_3_rh_native 45 51200 Net_8_ROIs_4_rh_native 46 8320 Net_8_ROIs_5_rh_native 47 25750 Net_8_ROIs_6_rh_native 48 1336330 Net_9_ROIs_1_rh_native 49 25740 Net_9_ROIs_2_rh_native 50 3983360 Net_9_ROIs_3_rh_native 51 7895160 Net_9_ROIs_4_rh_native 52 6553720 Net_9_ROIs_5_rh_native 53 8312 Net_9_ROIs_6_rh_native Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/rh.yeo2011.annot

---Annotations look fine.

Command: mri_label2vol --o lh.yeo2011_in_nat.mgz --annot ../lh.yeo2011.annot --identity --fill-ribbon --subject sub-DAEK --h emi lh

Output: Number of labels: 0 Annot File: ../lh.yeo2011.annot Template Volume: (null) Outut Volume: lh.yeo2011_in_nat.mgz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: sub-DAEK Hemi: lh UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects 7.2.0 INFO: loading surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.white nvertices = 253237 Reading thickness /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.thickness Loading annotations from ../lh.yeo2011.annot annotidmax = 48 nlabels = 48 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgz Mapping Segmentation fault

----Same thing occurs for the right hemi

On Wed, Jun 22, 2022 at 11:42 AM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,

Do you mean the issue that ‘mri_label2vol –fill-ribbon’ crashes? Can you re-run and provide your mris_label2annot and mri_label2vol command line and output?

I’m not sure I will be able to offer work around, but I would like to understand the problem better for future development.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Tuesday, June 21, 2022 5:04 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

It seems that this did not solve the issue. Are there any other reasons why this would occur?

Ben

On Fri, Jun 17, 2022 at 2:59 PM Benjamin Deck <bdeck8317@gmail.commailto:bdeck8317@gmail.com> wrote: Hi Yujing,

Thank you. I will give it a try! Can documentation be updated?

Ben

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On Fri, Jun 17, 2022 at 2:56 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,

Just wanted to update you on mris_label2annot command line options.

If ‘--no-unknown’ is used with mris_label2annot, ‘—offset 1’ should also be specified.

Yujing

From: Huang, Yujing Sent: Thursday, June 16, 2022 1:59 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: RE: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

Hi Ben,

I’m learning it myself too.

I played it a little more. I see the mismatch can happen if you skip a number in you LUT.

Also, if you have ‘0 Unknown 0 0 0 0’ in your LUT, I’m not sure you should use ‘--no-unknown’ for mris_label2annot. It will cause your annotation off by one.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Thursday, June 16, 2022 10:58 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

Thanks for taking a look. What do you mean by mismatch?

The LUT was used to make the annot file. What would generate this mismatch?

Here is the output from my mris_label2annot call:

mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --hemi lh Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 105 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 1 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_10_ROIs_1_lh_native.label 2 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_11_ROIs_1_lh_native.label 3 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_1_lh_native.label 4 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_2_lh_native.label 5 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_1_lh_native.label 6 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_2_lh_native.label 7 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_3_lh_native.label 8 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_4_lh_native.label 9 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_5_lh_native.label 10 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_1_lh_native.label 11 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_2_lh_native.label 12 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_3_lh_native.label 13 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_4_lh_native.label 14 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_5_lh_native.label 15 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_15_ROIs_1_lh_native.label 16 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_1_lh_native.label 17 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_2_lh_native.label 18 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_1_lh_native.label 19 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_2_lh_native.label 20 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_3_lh_native.label 21 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_4_lh_native.label 22 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_1_lh_native.label 23 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_2_lh_native.label 24 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_3_lh_native.label 25 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_4_lh_native.label 26 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_5_lh_native.label 27 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_19_ROIs_1_lh_native.label 28 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_1_lh_native.label 29 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_2_lh_native.label 30 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_1_lh_native.label 31 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_2_lh_native.label 32 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_3_lh_native.label 33 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_4_ROIs_1_lh_native.label 34 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_1_lh_native.label 35 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_2_lh_native.label 36 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_3_lh_native.label 37 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_4_lh_native.label 38 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_1_lh_native.label 39 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_2_lh_native.label 40 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_3_lh_native.label 41 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_1_lh_native.label 42 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_2_lh_native.label 43 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_1_lh_native.label 44 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_2_lh_native.label 45 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_3_lh_native.label 46 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_4_lh_native.label 47 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_5_lh_native.label 48 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_1_lh_native.label 49 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_2_lh_native.label 50 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_3_lh_native.label

7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --hemi lh sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 50 LabelThresh 0 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig 0 1336330 Net_10_ROIs_1_lh_native 1 1639705 Net_11_ROIs_1_lh_native 2 2647065 Net_12_ROIs_1_lh_native 3 11829830 Net_12_ROIs_2_lh_native 4 25700 Net_13_ROIs_1_lh_native 5 16399044 Net_13_ROIs_2_lh_native 6 6500 Net_13_ROIs_3_lh_native 7 3294840 Net_13_ROIs_4_lh_native 8 660700 Net_13_ROIs_5_lh_native 9 6558940 Net_14_ROIs_1_lh_native 10 7874740 Net_14_ROIs_2_lh_native 11 14465658 Net_14_ROIs_3_lh_native 12 9180300 Net_14_ROIs_4_lh_native 13 12300 Net_14_ROIs_5_lh_native 14 9182740 Net_15_ROIs_1_lh_native 15 3296035 Net_16_ROIs_1_lh_native 16 9211105 Net_16_ROIs_2_lh_native 17 4924360 Net_17_ROIs_1_lh_native 18 3302560 Net_17_ROIs_2_lh_native 19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native 21 13777468 Net_18_ROIs_1_lh_native 22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native 24 3294765 Net_18_ROIs_4_lh_native 25 14443610 Net_18_ROIs_5_lh_native 26 10511400 Net_19_ROIs_1_lh_native 27 8323072 Net_2_ROIs_1_lh_native 28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native 30 1316060 Net_3_ROIs_2_lh_native 31 14464220 Net_3_ROIs_3_lh_native 32 8323072 Net_4_ROIs_1_lh_native 33 7874740 Net_5_ROIs_1_lh_native 34 9180300 Net_5_ROIs_2_lh_native 35 8860211 Net_5_ROIs_3_lh_native 36 9182740 Net_5_ROIs_4_lh_native 37 3296035 Net_6_ROIs_1_lh_native 38 9211105 Net_6_ROIs_2_lh_native 39 4924360 Net_6_ROIs_3_lh_native 40 3302560 Net_7_ROIs_1_lh_native 41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native 45 3302620 Net_8_ROIs_4_lh_native 46 10811612 Net_8_ROIs_5_lh_native 47 2637020 Net_9_ROIs_1_lh_native 48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot

Thanks,

Ben

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On Tue, Jun 14, 2022 at 1:33 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,

I was able to reproduce the core dump. In my case, it was because a mismatch of color scheme between input annotation file and the color table loaded with the surface.

I suspect it might be the same issue for you too. But I’m not sure what the right action is to work around this.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Friday, June 10, 2022 11:47 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi there,

Having issues with the following command:

mri_label2vol --annot lh.yeo_2011.annot --temp /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz --hemi lh --fill-ribbon --identity --subject sub-DAEK --o lh.sub-DAEK_annot_nat.nii.gz

produces the following error:

Number of labels: 0 Annot File: lh.yeo_2011.annot Template Volume: /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz Outut Volume: lh.sub-DAEK_annot_nat.nii.gz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: sub-DAEK Hemi: lh UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects 7.2.0 Template RAS-to-Vox: -------- -1.25000 -0.00000 -0.00000 160.00000; -0.00000 -0.00000 -1.25000 160.00000; -0.00000 1.25000 -0.00000 160.00000; -0.00000 -0.00000 -0.00000 1.00000; Template Voxel Volume: 0.512 nHits Thresh: 0 Using Identity Matrix RegMat: -------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Label RAS-to-Vox: -------- -1.25000 0.00000 0.00000 160.00000; 0.00000 0.00000 -1.25000 160.00000; 0.00000 1.25000 0.00000 160.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.white nvertices = 253237 Reading thickness /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.thickness Loading annotations from lh.yeo_2011.annot annotidmax = 48 nlabels = 48 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgz Mapping Segmentation fault

But when I run the same command without fill-ribbon the process runs to completion.

Not sure if this is a memory issue or something else.

Ben

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University

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-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University

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-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1ohxFwDlj95GLWi92_zXWezKzkZSexk4R2BjNZnepB4disZNNuSpW1kK96h-7gzHWzHAfWDFB-dq5WFtrzogG_IDQxfKJM9_8THWm2gTlYr7E4JMzy50EQ0biIxFBc18A7TnYbRKYCW423M2Et_XUa845uEAbuqGRY-rPn8VINSo8n-KcLzZVfZIDWMcJfZiUh7nY6YlsjtlsatA_dXwilbQbksrtIoKDz9rGY5xmZZBLw_VbP8y8YHRyqOrPg4z8ic10lMUnmQgTlmAQ2YgWJ1xKBUPxs5Yk4ek3dLoLkM-g8rkKGlnK7y8aIl9YsPhk/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1gWC8FomBEWvS9SwG5Wk_5Npjvbjt5_29f_qSVE6r4gTYuQr1OZ3heuVWDhm6ygbJNNjl1rcmbLynrODhMW7zGVFOVKJuo9VGT_6ZzY4tD4lpW48h_e3rKiASiRE6iSmhswYQZU3h8c7vDBMokS0is2ROd2vxRcBpVk8R4coPUJm4HAxL7IJkyp9T1IOseEkAQ6Evmgof8igvqcLT9jVdvH6LXAARWQN8TW7ZoIwVtabTajMFOgP-2A0Kg_EmGcDvJqIrVwP2p0e0olstkbXWUkMW1IkROWarolKJ4h73QIjEXEmYKXqsMD_PaNG0quCB/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1gWC8FomBEWvS9SwG5Wk_5Npjvbjt5_29f_qSVE6r4gTYuQr1OZ3heuVWDhm6ygbJNNjl1rcmbLynrODhMW7zGVFOVKJuo9VGT_6ZzY4tD4lpW48h_e3rKiASiRE6iSmhswYQZU3h8c7vDBMokS0is2ROd2vxRcBpVk8R4coPUJm4HAxL7IJkyp9T1IOseEkAQ6Evmgof8igvqcLT9jVdvH6LXAARWQN8TW7ZoIwVtabTajMFOgP-2A0Kg_EmGcDvJqIrVwP2p0e0olstkbXWUkMW1IkROWarolKJ4h73QIjEXEmYKXqsMD_PaNG0quCB/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University

Hi Ben,

Based on your command line options (‘—no-unknown –offset 0’) and output, I believe your LUT starts with ‘0 Net_10_ROIs_1_lh_native 255 255 255 0’ not ‘0 Unknown 0 0 0 0’. Can you double check the LUT you passed to mris_label2annot?

I was able to reproduce the crash with duplicated color scheme scenario. Once you fix duplicated color schemes in your LUT, ‘mris_label2vol –fill-ribbon’ should run fine.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Benjamin Deck Sent: Thursday, June 23, 2022 10:42 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hmm.. I see what you're saying not the names but the actual location. Shouldn't I be getting a warning of overlapping labels and therefore an arg like --maxstatwinner would be helpful?

On Thu, Jun 23, 2022 at 10:34 AM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: For the duplicates, 19 is same as 41, 20 is same as 42, …

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Thursday, June 23, 2022 10:27 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

Thanks for your continued support on this issue.

Addressing your first question.

If I use --offset 1 then the get the following:

cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --offset 1 sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 50 LabelThresh 1 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig 1 1639705 Net_11_ROIs_1_lh_native 2 2647065 Net_12_ROIs_1_lh_native 3 11829830 Net_12_ROIs_2_lh_native 4 25700 Net_13_ROIs_1_lh_native 5 16399044 Net_13_ROIs_2_lh_native 6 6500 Net_13_ROIs_3_lh_native 7 3294840 Net_13_ROIs_4_lh_native 8 660700 Net_13_ROIs_5_lh_native 9 6558940 Net_14_ROIs_1_lh_native 10 7874740 Net_14_ROIs_2_lh_native 11 14465658 Net_14_ROIs_3_lh_native 12 9180300 Net_14_ROIs_4_lh_native 13 12300 Net_14_ROIs_5_lh_native 14 9182740 Net_15_ROIs_1_lh_native 15 3296035 Net_16_ROIs_1_lh_native 16 9211105 Net_16_ROIs_2_lh_native 17 4924360 Net_17_ROIs_1_lh_native 18 3302560 Net_17_ROIs_2_lh_native 19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native 21 13777468 Net_18_ROIs_1_lh_native 22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native 24 3294765 Net_18_ROIs_4_lh_native 25 14443610 Net_18_ROIs_5_lh_native 26 10511400 Net_19_ROIs_1_lh_native 27 8323072 Net_2_ROIs_1_lh_native 28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native 30 1316060 Net_3_ROIs_2_lh_native 31 14464220 Net_3_ROIs_3_lh_native 32 8323072 Net_4_ROIs_1_lh_native 33 7874740 Net_5_ROIs_1_lh_native 34 9180300 Net_5_ROIs_2_lh_native 35 8860211 Net_5_ROIs_3_lh_native 36 9182740 Net_5_ROIs_4_lh_native 37 3296035 Net_6_ROIs_1_lh_native 38 9211105 Net_6_ROIs_2_lh_native 39 4924360 Net_6_ROIs_3_lh_native 40 3302560 Net_7_ROIs_1_lh_native 41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native 45 3302620 Net_8_ROIs_4_lh_native 46 10811612 Net_8_ROIs_5_lh_native 47 2637020 Net_9_ROIs_1_lh_native 48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native 50 791413 cluster50 Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot

Where cluster50 is some nondescript cluster and it ignores my network 10 which should be the first entry.

To address your second question about duplicates.

19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native

While these may look almost like duplicates they are different rois within the same larger network. This separation is important for what I am doing so I need to keep the ROIs separate from one another but they are a part of the same larger network. However, Freesurfer doesn't know that they are.

On Thu, Jun 23, 2022 at 10:17 AM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: I am confused about ‘—no-unknown –offset 0’. Your output doesn’t seem agree with the codes. If your label starts at 1, I think it should be ‘—offset 1’ instead of 0. Can you double check your LUT?

I see duplicates in second column of these lines: (second column is calculated from RGB values.)

19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native

22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native

28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native

41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native

48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Thursday, June 23, 2022 9:36 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

I am not seeing any duplicates--highlighting wasn't rendered on my end.

my LUT:

0 Unknown 0 0 0 0 1 Net_10_ROIs_1_lh_native 255 255 255 0 2 Net_11_ROIs_1_lh_native 25 5 25 0 3 Net_12_ROIs_1_lh_native 25 100 40 0 4 Net_12_ROIs_2_lh_native 70 130 180 0 5 Net_13_ROIs_1_lh_native 100 100 0 0 6 Net_13_ROIs_2_lh_native 196 58 250 0

which is why I gave the --offset flag as 0 for --no-unknown

I did notice that the labels is incorrect. So for some reason, it seems to be missing two labels that exist in the annotation. That is strange.

Ben

On Thu, Jun 23, 2022 at 8:55 AM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: How does your LUT look like? What is your first line?

For left hemi, your loaded 50 label files to mris_label2annot, but mri_label2vol only reported 48 labels. It looks like you have duplicated RGB in your LUT. I have identified some. See highlighted in red. The duplicated RGB entries can cause problems.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Wednesday, June 22, 2022 2:24 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

Sure thing.

Commands:

mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt

Output: Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 105 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 1 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_10_ROIs_1_lh_native.label 2 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_11_ROIs_1_lh_native.label 3 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_1_lh_native.label 4 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_2_lh_native.label 5 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_1_lh_native.label 6 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_2_lh_native.label 7 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_3_lh_native.label 8 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_4_lh_native.label 9 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_5_lh_native.label 10 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_1_lh_native.label 11 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_2_lh_native.label 12 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_3_lh_native.label 13 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_4_lh_native.label 14 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_5_lh_native.label 15 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_15_ROIs_1_lh_native.label 16 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_1_lh_native.label 17 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_2_lh_native.label 18 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_1_lh_native.label 19 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_2_lh_native.label 20 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_3_lh_native.label 21 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_4_lh_native.label 22 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_1_lh_native.label 23 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_2_lh_native.label 24 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_3_lh_native.label 25 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_4_lh_native.label 26 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_5_lh_native.label 27 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_19_ROIs_1_lh_native.label 28 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_1_lh_native.label 29 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_2_lh_native.label 30 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_1_lh_native.label 31 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_2_lh_native.label 32 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_3_lh_native.label 33 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_4_ROIs_1_lh_native.label 34 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_1_lh_native.label 35 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_2_lh_native.label 36 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_3_lh_native.label 37 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_4_lh_native.label 38 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_1_lh_native.label 39 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_2_lh_native.label 40 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_3_lh_native.label 41 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_1_lh_native.label 42 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_2_lh_native.label 43 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_1_lh_native.label 44 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_2_lh_native.label 45 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_3_lh_native.label 46 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_4_lh_native.label 47 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_5_lh_native.label 48 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_1_lh_native.label 49 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_2_lh_native.label 50 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_3_lh_native.label

7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 50 LabelThresh 1 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig 0 16777215 Net_10_ROIs_1_lh_native 1 1639705 Net_11_ROIs_1_lh_native 2 2647065 Net_12_ROIs_1_lh_native 3 11829830 Net_12_ROIs_2_lh_native 4 25700 Net_13_ROIs_1_lh_native 5 16399044 Net_13_ROIs_2_lh_native 6 6500 Net_13_ROIs_3_lh_native 7 3294840 Net_13_ROIs_4_lh_native 8 660700 Net_13_ROIs_5_lh_native 9 6558940 Net_14_ROIs_1_lh_native 10 7874740 Net_14_ROIs_2_lh_native 11 14465658 Net_14_ROIs_3_lh_native 12 9180300 Net_14_ROIs_4_lh_native 13 12300 Net_14_ROIs_5_lh_native 14 9182740 Net_15_ROIs_1_lh_native 15 3296035 Net_16_ROIs_1_lh_native 16 9211105 Net_16_ROIs_2_lh_native 17 4924360 Net_17_ROIs_1_lh_native 18 3302560 Net_17_ROIs_2_lh_native 19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native 21 13777468 Net_18_ROIs_1_lh_native 22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native 24 3294765 Net_18_ROIs_4_lh_native 25 14443610 Net_18_ROIs_5_lh_native 26 10511400 Net_19_ROIs_1_lh_native 27 8323072 Net_2_ROIs_1_lh_native 28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native 30 1316060 Net_3_ROIs_2_lh_native 31 14464220 Net_3_ROIs_3_lh_native 32 8323072 Net_4_ROIs_1_lh_native 33 7874740 Net_5_ROIs_1_lh_native 34 9180300 Net_5_ROIs_2_lh_native 35 8860211 Net_5_ROIs_3_lh_native 36 9182740 Net_5_ROIs_4_lh_native 37 3296035 Net_6_ROIs_1_lh_native 38 9211105 Net_6_ROIs_2_lh_native 39 4924360 Net_6_ROIs_3_lh_native 40 3302560 Net_7_ROIs_1_lh_native 41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native 45 3302620 Net_8_ROIs_4_lh_native 46 10811612 Net_8_ROIs_5_lh_native 47 2637020 Net_9_ROIs_1_lh_native 48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot

command: mris_label2annot --s sub-DAEK --hemi rh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt

output: Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 105 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 51 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_10_ROIs_1_rh_native.label 52 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_11_ROIs_1_rh_native.label 53 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_12_ROIs_1_rh_native.label 54 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_12_ROIs_2_rh_native.label 55 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_1_rh_native.label 56 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_2_rh_native.label 57 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_3_rh_native.label 58 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_4_rh_native.label 59 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_1_rh_native.label 60 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_2_rh_native.label 61 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_3_rh_native.label 62 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_4_rh_native.label 63 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_5_rh_native.label 64 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_15_ROIs_1_rh_native.label 65 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_1_rh_native.label 66 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_2_rh_native.label 67 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_3_rh_native.label 68 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_1_rh_native.label 69 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_2_rh_native.label 70 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_3_rh_native.label 71 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_4_rh_native.label 72 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_1_rh_native.label 73 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_2_rh_native.label 74 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_3_rh_native.label 75 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_4_rh_native.label 76 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_19_ROIs_1_rh_native.label 77 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_2_ROIs_1_rh_native.label 78 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_2_ROIs_2_rh_native.label 79 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_1_rh_native.label 80 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_2_rh_native.label 81 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_3_rh_native.label 82 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_4_ROIs_1_rh_native.label 83 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_1_rh_native.label 84 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_2_rh_native.label 85 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_3_rh_native.label 86 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_4_rh_native.label 87 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_1_rh_native.label 88 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_2_rh_native.label 89 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_3_rh_native.label 90 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_1_rh_native.label 91 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_2_rh_native.label 92 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_3_rh_native.label 93 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_1_rh_native.label 94 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_2_rh_native.label 95 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_3_rh_native.label 96 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_4_rh_native.label 97 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_5_rh_native.label 98 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_6_rh_native.label 99 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_1_rh_native.label 100 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_2_rh_native.label 101 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_3_rh_native.label 102 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_4_rh_native.label 103 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_5_rh_native.label 104 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_6_rh_native.label

7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --hemi rh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi rh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 54 LabelThresh 1 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/rh.orig 0 1316060 Net_10_ROIs_1_rh_native 1 14464220 Net_11_ROIs_1_rh_native 2 14423100 Net_12_ROIs_1_rh_native 3 11832480 Net_12_ROIs_2_rh_native 4 9180240 Net_13_ROIs_1_rh_native 5 8204875 Net_13_ROIs_2_rh_native 6 10542100 Net_13_ROIs_3_rh_native 7 9231380 Net_13_ROIs_4_rh_native 8 9221140 Net_14_ROIs_1_rh_native 9 14474380 Net_14_ROIs_2_rh_native 10 2763429 Net_14_ROIs_3_rh_native 11 1351760 Net_14_ROIs_4_rh_native 12 15736992 Net_14_ROIs_5_rh_native 13 6553700 Net_15_ROIs_1_rh_native 14 11146310 Net_16_ROIs_1_rh_native 15 13145750 Net_16_ROIs_2_rh_native 16 3311482 Net_16_ROIs_3_rh_native 17 2146304 Net_17_ROIs_1_rh_native 18 5935475 Net_17_ROIs_2_rh_native 19 681085 Net_17_ROIs_3_rh_native 20 23060 Net_17_ROIs_4_rh_native 21 3957760 Net_18_ROIs_1_rh_native 22 3311482 Net_18_ROIs_2_rh_native 23 1321040 Net_18_ROIs_3_rh_native 24 3276922 Net_18_ROIs_4_rh_native 25 6588260 Net_19_ROIs_1_rh_native 26 3957760 Net_2_ROIs_1_rh_native 27 50372 Net_2_ROIs_2_rh_native 28 2671812 Net_3_ROIs_1_rh_native 29 3957956 Net_3_ROIs_2_rh_native 30 6564036 Net_3_ROIs_3_rh_native 31 3945156 Net_4_ROIs_1_rh_native 32 13127690 Net_5_ROIs_1_rh_native 33 6604880 Net_5_ROIs_2_rh_native 34 2647140 Net_5_ROIs_3_rh_native 35 3937480 Net_5_ROIs_4_rh_native 36 665610 Net_6_ROIs_1_rh_native 37 50372 Net_6_ROIs_2_rh_native 38 706590 Net_6_ROIs_3_rh_native 39 5923840 Net_7_ROIs_1_rh_native 40 6579200 Net_7_ROIs_2_rh_native 41 32768 Net_7_ROIs_3_rh_native 42 25600 Net_8_ROIs_1_rh_native 43 13117500 Net_8_ROIs_2_rh_native 44 6574090 Net_8_ROIs_3_rh_native 45 51200 Net_8_ROIs_4_rh_native 46 8320 Net_8_ROIs_5_rh_native 47 25750 Net_8_ROIs_6_rh_native 48 1336330 Net_9_ROIs_1_rh_native 49 25740 Net_9_ROIs_2_rh_native 50 3983360 Net_9_ROIs_3_rh_native 51 7895160 Net_9_ROIs_4_rh_native 52 6553720 Net_9_ROIs_5_rh_native 53 8312 Net_9_ROIs_6_rh_native Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/rh.yeo2011.annot

---Annotations look fine.

Command: mri_label2vol --o lh.yeo2011_in_nat.mgz --annot ../lh.yeo2011.annot --identity --fill-ribbon --subject sub-DAEK --h emi lh

Output: Number of labels: 0 Annot File: ../lh.yeo2011.annot Template Volume: (null) Outut Volume: lh.yeo2011_in_nat.mgz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: sub-DAEK Hemi: lh UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects 7.2.0 INFO: loading surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.white nvertices = 253237 Reading thickness /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.thickness Loading annotations from ../lh.yeo2011.annot annotidmax = 48 nlabels = 48 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgz Mapping Segmentation fault

----Same thing occurs for the right hemi

On Wed, Jun 22, 2022 at 11:42 AM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,

Do you mean the issue that ‘mri_label2vol –fill-ribbon’ crashes? Can you re-run and provide your mris_label2annot and mri_label2vol command line and output?

I’m not sure I will be able to offer work around, but I would like to understand the problem better for future development.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Tuesday, June 21, 2022 5:04 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

It seems that this did not solve the issue. Are there any other reasons why this would occur?

Ben

On Fri, Jun 17, 2022 at 2:59 PM Benjamin Deck <bdeck8317@gmail.commailto:bdeck8317@gmail.com> wrote: Hi Yujing,

Thank you. I will give it a try! Can documentation be updated?

Ben

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On Fri, Jun 17, 2022 at 2:56 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,

Just wanted to update you on mris_label2annot command line options.

If ‘--no-unknown’ is used with mris_label2annot, ‘—offset 1’ should also be specified.

Yujing

From: Huang, Yujing Sent: Thursday, June 16, 2022 1:59 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: RE: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

Hi Ben,

I’m learning it myself too.

I played it a little more. I see the mismatch can happen if you skip a number in you LUT.

Also, if you have ‘0 Unknown 0 0 0 0’ in your LUT, I’m not sure you should use ‘--no-unknown’ for mris_label2annot. It will cause your annotation off by one.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Thursday, June 16, 2022 10:58 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

Thanks for taking a look. What do you mean by mismatch?

The LUT was used to make the annot file. What would generate this mismatch?

Here is the output from my mris_label2annot call:

mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --hemi lh Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 105 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 1 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_10_ROIs_1_lh_native.label 2 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_11_ROIs_1_lh_native.label 3 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_1_lh_native.label 4 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_2_lh_native.label 5 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_1_lh_native.label 6 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_2_lh_native.label 7 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_3_lh_native.label 8 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_4_lh_native.label 9 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_5_lh_native.label 10 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_1_lh_native.label 11 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_2_lh_native.label 12 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_3_lh_native.label 13 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_4_lh_native.label 14 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_5_lh_native.label 15 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_15_ROIs_1_lh_native.label 16 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_1_lh_native.label 17 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_2_lh_native.label 18 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_1_lh_native.label 19 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_2_lh_native.label 20 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_3_lh_native.label 21 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_4_lh_native.label 22 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_1_lh_native.label 23 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_2_lh_native.label 24 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_3_lh_native.label 25 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_4_lh_native.label 26 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_5_lh_native.label 27 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_19_ROIs_1_lh_native.label 28 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_1_lh_native.label 29 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_2_lh_native.label 30 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_1_lh_native.label 31 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_2_lh_native.label 32 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_3_lh_native.label 33 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_4_ROIs_1_lh_native.label 34 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_1_lh_native.label 35 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_2_lh_native.label 36 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_3_lh_native.label 37 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_4_lh_native.label 38 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_1_lh_native.label 39 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_2_lh_native.label 40 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_3_lh_native.label 41 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_1_lh_native.label 42 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_2_lh_native.label 43 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_1_lh_native.label 44 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_2_lh_native.label 45 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_3_lh_native.label 46 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_4_lh_native.label 47 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_5_lh_native.label 48 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_1_lh_native.label 49 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_2_lh_native.label 50 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_3_lh_native.label

7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --hemi lh sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 50 LabelThresh 0 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig 0 1336330 Net_10_ROIs_1_lh_native 1 1639705 Net_11_ROIs_1_lh_native 2 2647065 Net_12_ROIs_1_lh_native 3 11829830 Net_12_ROIs_2_lh_native 4 25700 Net_13_ROIs_1_lh_native 5 16399044 Net_13_ROIs_2_lh_native 6 6500 Net_13_ROIs_3_lh_native 7 3294840 Net_13_ROIs_4_lh_native 8 660700 Net_13_ROIs_5_lh_native 9 6558940 Net_14_ROIs_1_lh_native 10 7874740 Net_14_ROIs_2_lh_native 11 14465658 Net_14_ROIs_3_lh_native 12 9180300 Net_14_ROIs_4_lh_native 13 12300 Net_14_ROIs_5_lh_native 14 9182740 Net_15_ROIs_1_lh_native 15 3296035 Net_16_ROIs_1_lh_native 16 9211105 Net_16_ROIs_2_lh_native 17 4924360 Net_17_ROIs_1_lh_native 18 3302560 Net_17_ROIs_2_lh_native 19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native 21 13777468 Net_18_ROIs_1_lh_native 22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native 24 3294765 Net_18_ROIs_4_lh_native 25 14443610 Net_18_ROIs_5_lh_native 26 10511400 Net_19_ROIs_1_lh_native 27 8323072 Net_2_ROIs_1_lh_native 28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native 30 1316060 Net_3_ROIs_2_lh_native 31 14464220 Net_3_ROIs_3_lh_native 32 8323072 Net_4_ROIs_1_lh_native 33 7874740 Net_5_ROIs_1_lh_native 34 9180300 Net_5_ROIs_2_lh_native 35 8860211 Net_5_ROIs_3_lh_native 36 9182740 Net_5_ROIs_4_lh_native 37 3296035 Net_6_ROIs_1_lh_native 38 9211105 Net_6_ROIs_2_lh_native 39 4924360 Net_6_ROIs_3_lh_native 40 3302560 Net_7_ROIs_1_lh_native 41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native 45 3302620 Net_8_ROIs_4_lh_native 46 10811612 Net_8_ROIs_5_lh_native 47 2637020 Net_9_ROIs_1_lh_native 48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot

Thanks,

Ben

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On Tue, Jun 14, 2022 at 1:33 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,

I was able to reproduce the core dump. In my case, it was because a mismatch of color scheme between input annotation file and the color table loaded with the surface.

I suspect it might be the same issue for you too. But I’m not sure what the right action is to work around this.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Friday, June 10, 2022 11:47 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi there,

Having issues with the following command:

mri_label2vol --annot lh.yeo_2011.annot --temp /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz --hemi lh --fill-ribbon --identity --subject sub-DAEK --o lh.sub-DAEK_annot_nat.nii.gz

produces the following error:

Number of labels: 0 Annot File: lh.yeo_2011.annot Template Volume: /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz Outut Volume: lh.sub-DAEK_annot_nat.nii.gz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: sub-DAEK Hemi: lh UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects 7.2.0 Template RAS-to-Vox: -------- -1.25000 -0.00000 -0.00000 160.00000; -0.00000 -0.00000 -1.25000 160.00000; -0.00000 1.25000 -0.00000 160.00000; -0.00000 -0.00000 -0.00000 1.00000; Template Voxel Volume: 0.512 nHits Thresh: 0 Using Identity Matrix RegMat: -------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Label RAS-to-Vox: -------- -1.25000 0.00000 0.00000 160.00000; 0.00000 0.00000 -1.25000 160.00000; 0.00000 1.25000 0.00000 160.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.white nvertices = 253237 Reading thickness /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.thickness Loading annotations from lh.yeo_2011.annot annotidmax = 48 nlabels = 48 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgz Mapping Segmentation fault

But when I run the same command without fill-ribbon the process runs to completion.

Not sure if this is a memory issue or something else.

Ben

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University

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-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University

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-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1ohxFwDlj95GLWi92_zXWezKzkZSexk4R2BjNZnepB4disZNNuSpW1kK96h-7gzHWzHAfWDFB-dq5WFtrzogG_IDQxfKJM9_8THWm2gTlYr7E4JMzy50EQ0biIxFBc18A7TnYbRKYCW423M2Et_XUa845uEAbuqGRY-rPn8VINSo8n-KcLzZVfZIDWMcJfZiUh7nY6YlsjtlsatA_dXwilbQbksrtIoKDz9rGY5xmZZBLw_VbP8y8YHRyqOrPg4z8ic10lMUnmQgTlmAQ2YgWJ1xKBUPxs5Yk4ek3dLoLkM-g8rkKGlnK7y8aIl9YsPhk/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1gWC8FomBEWvS9SwG5Wk_5Npjvbjt5_29f_qSVE6r4gTYuQr1OZ3heuVWDhm6ygbJNNjl1rcmbLynrODhMW7zGVFOVKJuo9VGT_6ZzY4tD4lpW48h_e3rKiASiRE6iSmhswYQZU3h8c7vDBMokS0is2ROd2vxRcBpVk8R4coPUJm4HAxL7IJkyp9T1IOseEkAQ6Evmgof8igvqcLT9jVdvH6LXAARWQN8TW7ZoIwVtabTajMFOgP-2A0Kg_EmGcDvJqIrVwP2p0e0olstkbXWUkMW1IkROWarolKJ4h73QIjEXEmYKXqsMD_PaNG0quCB/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1gWC8FomBEWvS9SwG5Wk_5Npjvbjt5_29f_qSVE6r4gTYuQr1OZ3heuVWDhm6ygbJNNjl1rcmbLynrODhMW7zGVFOVKJuo9VGT_6ZzY4tD4lpW48h_e3rKiASiRE6iSmhswYQZU3h8c7vDBMokS0is2ROd2vxRcBpVk8R4coPUJm4HAxL7IJkyp9T1IOseEkAQ6Evmgof8igvqcLT9jVdvH6LXAARWQN8TW7ZoIwVtabTajMFOgP-2A0Kg_EmGcDvJqIrVwP2p0e0olstkbXWUkMW1IkROWarolKJ4h73QIjEXEmYKXqsMD_PaNG0quCB/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1-Co0Tj3nO9PKVc4FF5EYp-pbwW1MSBhpVRo4lPgCIr_Le-jinRghImfaUz1XwH3bS9-3JJtGF7iqyCINnenimFyLBFGtPvkx4gKT4LM_XuqtA8yehAilreaW-7tfG7rFm9CKmyvL6UTMUL8ixh3tIeZDVlTa-WL09UQo8OB3xQPLEOyeBBTdvYOD9-EejJcMmPhvCbVyM7VATQc4WnF3BT3C9Wr5Fp2UY25cbOG0IiS9S3TID8jUqddMj_O_8SHKh8odIuW_MNbPu35lVuaMTi9Gh9V0u7p3tOIkH4vOTMN-8GTlTCP5safglQWXvSSt/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1nUKsaivbAuxJojvr0yFs7hY0LXQON0_HrlCUPtW5ymN-QLI0xMSE64vbmxo74tTH5VaFyluU46uvw3l-Oi9Zs6J_C9ApmKC6YBCM7Vp9dxkgV2G-JQiYfsxps_neYqUYs3Ex6cqTkpvxd29lBZXFfOAAEuEh89KJ9t3RbBTeOlzXr_mxGPrA9_wXx5Ik_NMVLgPT_qhUj3n03BUZBWoYAS8fR1HG-dDJAvMSNEIbB4DEEaIO1w4toFS_NkYAtb0_kF5ch2aEyPtKeAXZXAQNHORaUhvK4OmoxzwZuVrxEFBj3kjicTmAplnxy8Ns7pjx/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1nUKsaivbAuxJojvr0yFs7hY0LXQON0_HrlCUPtW5ymN-QLI0xMSE64vbmxo74tTH5VaFyluU46uvw3l-Oi9Zs6J_C9ApmKC6YBCM7Vp9dxkgV2G-JQiYfsxps_neYqUYs3Ex6cqTkpvxd29lBZXFfOAAEuEh89KJ9t3RbBTeOlzXr_mxGPrA9_wXx5Ik_NMVLgPT_qhUj3n03BUZBWoYAS8fR1HG-dDJAvMSNEIbB4DEEaIO1w4toFS_NkYAtb0_kF5ch2aEyPtKeAXZXAQNHORaUhvK4OmoxzwZuVrxEFBj3kjicTmAplnxy8Ns7pjx/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1vY_16Zjww2xu0uzWyiUohSSGGRD2H3nPfBx-WboNIK-KoK15rtSqkX2N-vmZ_cZ27ff2CpMOXLf512LEyZ_evkkY3h5Fj3fd8kZmWMbNzbz13qEX-J_IC_P6asO8e2VQ_smAoIOlIkFkOJHjdqGr04XT2bVWuPZjC9dOlUH26F47LauKhAEPdxCKLr4NE9Pv3ivq0eZZ5kFH0bqLzGyz0nNRpBvXgkwvnlq8hqiHZ8Bxe0h2o9TE0GEYSMPGRmj3BKHyBYVGLsX58dmumT-cSW8AEvkCb91oK2Lv-DywOJBySAA4UnwaUtsPVsa-Qaz80DhUEKpRssMKaD0KwpO1-Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1KyPIPmRNwus-z79lEGn0T7diD2lNJqoI2KIQh4lMv2faOIlvJOXCKLsN35WtRkxw61rareTh_XeaqS274mShL_BwFF0zrupuNsCOKEU94cyu7wYoAM6A93LTuYfY69rB1_3laFePNZaecZtHzcaAqoooOI2HEKJu89TZc6ronKly_Y7oIPveyaULOt3u4wFYCT2PowbhyLRJ5rEfGIkGksjlIxIB46ynWAQuDbi1KJPj7YPc039Tros_bYxNL_UjuGzrk_VVjobmcicqBvJbHh69MPWijPmHDSLTSx76IPcDo85-lkMmm_-3yhZXEoMMFwMXN-kGs8rg9zY0wYgyNQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1KyPIPmRNwus-z79lEGn0T7diD2lNJqoI2KIQh4lMv2faOIlvJOXCKLsN35WtRkxw61rareTh_XeaqS274mShL_BwFF0zrupuNsCOKEU94cyu7wYoAM6A93LTuYfY69rB1_3laFePNZaecZtHzcaAqoooOI2HEKJu89TZc6ronKly_Y7oIPveyaULOt3u4wFYCT2PowbhyLRJ5rEfGIkGksjlIxIB46ynWAQuDbi1KJPj7YPc039Tros_bYxNL_UjuGzrk_VVjobmcicqBvJbHh69MPWijPmHDSLTSx76IPcDo85-lkMmm_-3yhZXEoMMFwMXN-kGs8rg9zY0wYgyNQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University

I noticed two things: 1. you have skipped numbers in label files output - make sure all label names in LUT have corresponding label files hemi.label-name.label in ldir directory. 2. your annotation output doesn’t agree with the LUT your showed - make sure you are passing the correct copy to mris_label2annot

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Benjamin Deck Sent: Friday, June 24, 2022 4:47 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

I just re-ran this and I am now noticing something else that is strange.

I included an "unknown 0 0 0 0" row at the beginning and gave this a 0 index. Similar to the default LUT

LUT: 0 Unknown 255 255 255 0 1 Net_14_ROIs_4_native 25 5 25 0 2 Net_9_ROIs_1_native 25 100 40 0 3 Net_18_ROIs_4_native 70 130 180 0

My command and output:

mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --ctab sub-DAEK_yeoLUT.txt --maxstatwinner --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019/ Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 57 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 1 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_14_ROIs_4_native.label 2 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_9_ROIs_1_native.label 3 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_18_ROIs_4_native.label 4 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_8_ROIs_1_native.label 5 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_14_ROIs_1_native.label 7 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_14_ROIs_2_native.label 8 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_6_ROIs_1_native.label 10 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_9_ROIs_2_native.label 11 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_8_ROIs_3_native.label 12 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_17_ROIs_3_native.label 13 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_10_ROIs_1_native.label 14 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_5_ROIs_3_native.label 15 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_16_ROIs_2_native.label 16 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_5_ROIs_4_native.label 17 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_9_ROIs_3_native.label 18 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_18_ROIs_3_native.label 20 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_13_ROIs_2_native.label 21 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_2_ROIs_1_native.label 23 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_5_ROIs_1_native.label 24 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_13_ROIs_1_native.label 25 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_8_ROIs_4_native.label 26 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_13_ROIs_3_native.label 27 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_8_ROIs_2_native.label 28 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_18_ROIs_5_native.label 29 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_17_ROIs_2_native.label 30 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_12_ROIs_1_native.label 31 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_3_ROIs_3_native.label 32 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_18_ROIs_1_native.label 33 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_11_ROIs_1_native.label 35 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_3_ROIs_2_native.label 36 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_6_ROIs_2_native.label 37 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_13_ROIs_4_native.label 39 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_15_ROIs_1_native.label 40 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_7_ROIs_1_native.label 41 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_18_ROIs_2_native.label 42 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_19_ROIs_1_native.label 43 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_2_ROIs_2_native.label 44 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_5_ROIs_2_native.label 45 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_16_ROIs_1_native.label 46 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_14_ROIs_5_native.label 47 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_13_ROIs_5_native.label 48 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_3_ROIs_1_native.label 49 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_7_ROIs_2_native.label 50 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_12_ROIs_2_native.label 51 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_8_ROIs_5_native.label 52 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_17_ROIs_4_native.label 53 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_4_ROIs_1_native.label 54 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_17_ROIs_1_native.label 55 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_14_ROIs_3_native.label 56 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_6_ROIs_3_native.label

7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019 cmdline mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --ctab sub-DAEK_yeoLUT.txt --maxstatwinner --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019/ sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 50 LabelThresh 0 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig 1 2647065 Net_9_ROIs_1_native 2 11829830 Net_18_ROIs_4_native 3 25700 Net_8_ROIs_1_native 4 16399044 Net_14_ROIs_1_native 5 3294840 Net_14_ROIs_2_native 6 660700 Net_6_ROIs_1_native 7 7874740 Net_9_ROIs_2_native 8 14465658 Net_8_ROIs_3_native 9 9180300 Net_17_ROIs_3_native 10 12300 Net_10_ROIs_1_native 11 9182740 Net_5_ROIs_3_native 12 3296035 Net_16_ROIs_2_native 13 9211105 Net_5_ROIs_4_native 14 4924360 Net_9_ROIs_3_native 15 3302560 Net_18_ROIs_3_native 16 3988540 Net_13_ROIs_2_native 17 13777468 Net_2_ROIs_1_native 18 3302420 Net_5_ROIs_1_native 19 3294765 Net_13_ROIs_1_native 20 14443610 Net_8_ROIs_4_native 21 10511400 Net_13_ROIs_3_native 22 8323072 Net_8_ROIs_2_native 23 1326300 Net_18_ROIs_5_native 24 3957880 Net_17_ROIs_2_native 25 1316060 Net_12_ROIs_1_native 26 14464220 Net_3_ROIs_3_native 27 8323072 Net_18_ROIs_1_native 28 7874740 Net_11_ROIs_1_native 29 8860211 Net_3_ROIs_2_native 30 9182740 Net_6_ROIs_2_native 31 3296035 Net_13_ROIs_4_native 32 4924360 Net_15_ROIs_1_native 33 3302560 Net_7_ROIs_1_native 34 3988500 Net_18_ROIs_2_native 35 3988540 Net_19_ROIs_1_native 36 9221340 Net_2_ROIs_2_native 37 3302420 Net_5_ROIs_2_native 38 3302620 Net_16_ROIs_1_native 39 10811612 Net_14_ROIs_5_native 40 2637020 Net_13_ROIs_5_native 41 1326300 Net_3_ROIs_1_native 42 3957880 Net_7_ROIs_2_native 43 1316060 Net_12_ROIs_2_native 44 14464220 Net_8_ROIs_5_native 45 14423100 Net_17_ROIs_4_native 46 11832480 Net_4_ROIs_1_native 47 9180240 Net_17_ROIs_1_native 48 8204875 Net_14_ROIs_3_native 49 10542100 Net_6_ROIs_3_native 50 3840729 cluster50 Mapping unhit to unknown Found 19023 unhit vertices Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot

For some very weird reason it skips my 0 row, 'unknown' and then adds an undescript cluster at the end.

Why is that occurring?

Ben

On Fri, Jun 24, 2022 at 4:00 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,

Based on your command line options (‘—no-unknown –offset 0’) and output, I believe your LUT starts with ‘0 Net_10_ROIs_1_lh_native 255 255 255 0’ not ‘0 Unknown 0 0 0 0’. Can you double check the LUT you passed to mris_label2annot?

I was able to reproduce the crash with duplicated color scheme scenario. Once you fix duplicated color schemes in your LUT, ‘mris_label2vol –fill-ribbon’ should run fine.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Thursday, June 23, 2022 10:42 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hmm.. I see what you're saying not the names but the actual location. Shouldn't I be getting a warning of overlapping labels and therefore an arg like --maxstatwinner would be helpful?

On Thu, Jun 23, 2022 at 10:34 AM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: For the duplicates, 19 is same as 41, 20 is same as 42, …

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Thursday, June 23, 2022 10:27 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

Thanks for your continued support on this issue.

Addressing your first question.

If I use --offset 1 then the get the following:

cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --offset 1 sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 50 LabelThresh 1 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig 1 1639705 Net_11_ROIs_1_lh_native 2 2647065 Net_12_ROIs_1_lh_native 3 11829830 Net_12_ROIs_2_lh_native 4 25700 Net_13_ROIs_1_lh_native 5 16399044 Net_13_ROIs_2_lh_native 6 6500 Net_13_ROIs_3_lh_native 7 3294840 Net_13_ROIs_4_lh_native 8 660700 Net_13_ROIs_5_lh_native 9 6558940 Net_14_ROIs_1_lh_native 10 7874740 Net_14_ROIs_2_lh_native 11 14465658 Net_14_ROIs_3_lh_native 12 9180300 Net_14_ROIs_4_lh_native 13 12300 Net_14_ROIs_5_lh_native 14 9182740 Net_15_ROIs_1_lh_native 15 3296035 Net_16_ROIs_1_lh_native 16 9211105 Net_16_ROIs_2_lh_native 17 4924360 Net_17_ROIs_1_lh_native 18 3302560 Net_17_ROIs_2_lh_native 19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native 21 13777468 Net_18_ROIs_1_lh_native 22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native 24 3294765 Net_18_ROIs_4_lh_native 25 14443610 Net_18_ROIs_5_lh_native 26 10511400 Net_19_ROIs_1_lh_native 27 8323072 Net_2_ROIs_1_lh_native 28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native 30 1316060 Net_3_ROIs_2_lh_native 31 14464220 Net_3_ROIs_3_lh_native 32 8323072 Net_4_ROIs_1_lh_native 33 7874740 Net_5_ROIs_1_lh_native 34 9180300 Net_5_ROIs_2_lh_native 35 8860211 Net_5_ROIs_3_lh_native 36 9182740 Net_5_ROIs_4_lh_native 37 3296035 Net_6_ROIs_1_lh_native 38 9211105 Net_6_ROIs_2_lh_native 39 4924360 Net_6_ROIs_3_lh_native 40 3302560 Net_7_ROIs_1_lh_native 41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native 45 3302620 Net_8_ROIs_4_lh_native 46 10811612 Net_8_ROIs_5_lh_native 47 2637020 Net_9_ROIs_1_lh_native 48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native 50 791413 cluster50 Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot

Where cluster50 is some nondescript cluster and it ignores my network 10 which should be the first entry.

To address your second question about duplicates.

19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native

While these may look almost like duplicates they are different rois within the same larger network. This separation is important for what I am doing so I need to keep the ROIs separate from one another but they are a part of the same larger network. However, Freesurfer doesn't know that they are.

On Thu, Jun 23, 2022 at 10:17 AM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: I am confused about ‘—no-unknown –offset 0’. Your output doesn’t seem agree with the codes. If your label starts at 1, I think it should be ‘—offset 1’ instead of 0. Can you double check your LUT?

I see duplicates in second column of these lines: (second column is calculated from RGB values.)

19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native

22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native

28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native

41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native

48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Thursday, June 23, 2022 9:36 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

I am not seeing any duplicates--highlighting wasn't rendered on my end.

my LUT:

0 Unknown 0 0 0 0 1 Net_10_ROIs_1_lh_native 255 255 255 0 2 Net_11_ROIs_1_lh_native 25 5 25 0 3 Net_12_ROIs_1_lh_native 25 100 40 0 4 Net_12_ROIs_2_lh_native 70 130 180 0 5 Net_13_ROIs_1_lh_native 100 100 0 0 6 Net_13_ROIs_2_lh_native 196 58 250 0

which is why I gave the --offset flag as 0 for --no-unknown

I did notice that the labels is incorrect. So for some reason, it seems to be missing two labels that exist in the annotation. That is strange.

Ben

On Thu, Jun 23, 2022 at 8:55 AM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: How does your LUT look like? What is your first line?

For left hemi, your loaded 50 label files to mris_label2annot, but mri_label2vol only reported 48 labels. It looks like you have duplicated RGB in your LUT. I have identified some. See highlighted in red. The duplicated RGB entries can cause problems.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Wednesday, June 22, 2022 2:24 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

Sure thing.

Commands:

mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt

Output: Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 105 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 1 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_10_ROIs_1_lh_native.label 2 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_11_ROIs_1_lh_native.label 3 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_1_lh_native.label 4 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_2_lh_native.label 5 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_1_lh_native.label 6 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_2_lh_native.label 7 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_3_lh_native.label 8 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_4_lh_native.label 9 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_5_lh_native.label 10 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_1_lh_native.label 11 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_2_lh_native.label 12 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_3_lh_native.label 13 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_4_lh_native.label 14 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_5_lh_native.label 15 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_15_ROIs_1_lh_native.label 16 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_1_lh_native.label 17 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_2_lh_native.label 18 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_1_lh_native.label 19 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_2_lh_native.label 20 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_3_lh_native.label 21 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_4_lh_native.label 22 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_1_lh_native.label 23 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_2_lh_native.label 24 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_3_lh_native.label 25 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_4_lh_native.label 26 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_5_lh_native.label 27 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_19_ROIs_1_lh_native.label 28 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_1_lh_native.label 29 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_2_lh_native.label 30 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_1_lh_native.label 31 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_2_lh_native.label 32 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_3_lh_native.label 33 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_4_ROIs_1_lh_native.label 34 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_1_lh_native.label 35 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_2_lh_native.label 36 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_3_lh_native.label 37 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_4_lh_native.label 38 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_1_lh_native.label 39 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_2_lh_native.label 40 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_3_lh_native.label 41 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_1_lh_native.label 42 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_2_lh_native.label 43 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_1_lh_native.label 44 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_2_lh_native.label 45 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_3_lh_native.label 46 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_4_lh_native.label 47 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_5_lh_native.label 48 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_1_lh_native.label 49 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_2_lh_native.label 50 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_3_lh_native.label

7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 50 LabelThresh 1 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig 0 16777215 Net_10_ROIs_1_lh_native 1 1639705 Net_11_ROIs_1_lh_native 2 2647065 Net_12_ROIs_1_lh_native 3 11829830 Net_12_ROIs_2_lh_native 4 25700 Net_13_ROIs_1_lh_native 5 16399044 Net_13_ROIs_2_lh_native 6 6500 Net_13_ROIs_3_lh_native 7 3294840 Net_13_ROIs_4_lh_native 8 660700 Net_13_ROIs_5_lh_native 9 6558940 Net_14_ROIs_1_lh_native 10 7874740 Net_14_ROIs_2_lh_native 11 14465658 Net_14_ROIs_3_lh_native 12 9180300 Net_14_ROIs_4_lh_native 13 12300 Net_14_ROIs_5_lh_native 14 9182740 Net_15_ROIs_1_lh_native 15 3296035 Net_16_ROIs_1_lh_native 16 9211105 Net_16_ROIs_2_lh_native 17 4924360 Net_17_ROIs_1_lh_native 18 3302560 Net_17_ROIs_2_lh_native 19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native 21 13777468 Net_18_ROIs_1_lh_native 22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native 24 3294765 Net_18_ROIs_4_lh_native 25 14443610 Net_18_ROIs_5_lh_native 26 10511400 Net_19_ROIs_1_lh_native 27 8323072 Net_2_ROIs_1_lh_native 28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native 30 1316060 Net_3_ROIs_2_lh_native 31 14464220 Net_3_ROIs_3_lh_native 32 8323072 Net_4_ROIs_1_lh_native 33 7874740 Net_5_ROIs_1_lh_native 34 9180300 Net_5_ROIs_2_lh_native 35 8860211 Net_5_ROIs_3_lh_native 36 9182740 Net_5_ROIs_4_lh_native 37 3296035 Net_6_ROIs_1_lh_native 38 9211105 Net_6_ROIs_2_lh_native 39 4924360 Net_6_ROIs_3_lh_native 40 3302560 Net_7_ROIs_1_lh_native 41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native 45 3302620 Net_8_ROIs_4_lh_native 46 10811612 Net_8_ROIs_5_lh_native 47 2637020 Net_9_ROIs_1_lh_native 48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot

command: mris_label2annot --s sub-DAEK --hemi rh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt

output: Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 105 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 51 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_10_ROIs_1_rh_native.label 52 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_11_ROIs_1_rh_native.label 53 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_12_ROIs_1_rh_native.label 54 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_12_ROIs_2_rh_native.label 55 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_1_rh_native.label 56 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_2_rh_native.label 57 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_3_rh_native.label 58 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_4_rh_native.label 59 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_1_rh_native.label 60 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_2_rh_native.label 61 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_3_rh_native.label 62 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_4_rh_native.label 63 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_5_rh_native.label 64 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_15_ROIs_1_rh_native.label 65 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_1_rh_native.label 66 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_2_rh_native.label 67 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_3_rh_native.label 68 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_1_rh_native.label 69 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_2_rh_native.label 70 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_3_rh_native.label 71 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_4_rh_native.label 72 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_1_rh_native.label 73 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_2_rh_native.label 74 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_3_rh_native.label 75 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_4_rh_native.label 76 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_19_ROIs_1_rh_native.label 77 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_2_ROIs_1_rh_native.label 78 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_2_ROIs_2_rh_native.label 79 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_1_rh_native.label 80 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_2_rh_native.label 81 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_3_rh_native.label 82 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_4_ROIs_1_rh_native.label 83 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_1_rh_native.label 84 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_2_rh_native.label 85 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_3_rh_native.label 86 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_4_rh_native.label 87 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_1_rh_native.label 88 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_2_rh_native.label 89 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_3_rh_native.label 90 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_1_rh_native.label 91 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_2_rh_native.label 92 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_3_rh_native.label 93 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_1_rh_native.label 94 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_2_rh_native.label 95 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_3_rh_native.label 96 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_4_rh_native.label 97 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_5_rh_native.label 98 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_6_rh_native.label 99 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_1_rh_native.label 100 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_2_rh_native.label 101 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_3_rh_native.label 102 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_4_rh_native.label 103 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_5_rh_native.label 104 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_6_rh_native.label

7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --hemi rh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi rh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 54 LabelThresh 1 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/rh.orig 0 1316060 Net_10_ROIs_1_rh_native 1 14464220 Net_11_ROIs_1_rh_native 2 14423100 Net_12_ROIs_1_rh_native 3 11832480 Net_12_ROIs_2_rh_native 4 9180240 Net_13_ROIs_1_rh_native 5 8204875 Net_13_ROIs_2_rh_native 6 10542100 Net_13_ROIs_3_rh_native 7 9231380 Net_13_ROIs_4_rh_native 8 9221140 Net_14_ROIs_1_rh_native 9 14474380 Net_14_ROIs_2_rh_native 10 2763429 Net_14_ROIs_3_rh_native 11 1351760 Net_14_ROIs_4_rh_native 12 15736992 Net_14_ROIs_5_rh_native 13 6553700 Net_15_ROIs_1_rh_native 14 11146310 Net_16_ROIs_1_rh_native 15 13145750 Net_16_ROIs_2_rh_native 16 3311482 Net_16_ROIs_3_rh_native 17 2146304 Net_17_ROIs_1_rh_native 18 5935475 Net_17_ROIs_2_rh_native 19 681085 Net_17_ROIs_3_rh_native 20 23060 Net_17_ROIs_4_rh_native 21 3957760 Net_18_ROIs_1_rh_native 22 3311482 Net_18_ROIs_2_rh_native 23 1321040 Net_18_ROIs_3_rh_native 24 3276922 Net_18_ROIs_4_rh_native 25 6588260 Net_19_ROIs_1_rh_native 26 3957760 Net_2_ROIs_1_rh_native 27 50372 Net_2_ROIs_2_rh_native 28 2671812 Net_3_ROIs_1_rh_native 29 3957956 Net_3_ROIs_2_rh_native 30 6564036 Net_3_ROIs_3_rh_native 31 3945156 Net_4_ROIs_1_rh_native 32 13127690 Net_5_ROIs_1_rh_native 33 6604880 Net_5_ROIs_2_rh_native 34 2647140 Net_5_ROIs_3_rh_native 35 3937480 Net_5_ROIs_4_rh_native 36 665610 Net_6_ROIs_1_rh_native 37 50372 Net_6_ROIs_2_rh_native 38 706590 Net_6_ROIs_3_rh_native 39 5923840 Net_7_ROIs_1_rh_native 40 6579200 Net_7_ROIs_2_rh_native 41 32768 Net_7_ROIs_3_rh_native 42 25600 Net_8_ROIs_1_rh_native 43 13117500 Net_8_ROIs_2_rh_native 44 6574090 Net_8_ROIs_3_rh_native 45 51200 Net_8_ROIs_4_rh_native 46 8320 Net_8_ROIs_5_rh_native 47 25750 Net_8_ROIs_6_rh_native 48 1336330 Net_9_ROIs_1_rh_native 49 25740 Net_9_ROIs_2_rh_native 50 3983360 Net_9_ROIs_3_rh_native 51 7895160 Net_9_ROIs_4_rh_native 52 6553720 Net_9_ROIs_5_rh_native 53 8312 Net_9_ROIs_6_rh_native Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/rh.yeo2011.annot

---Annotations look fine.

Command: mri_label2vol --o lh.yeo2011_in_nat.mgz --annot ../lh.yeo2011.annot --identity --fill-ribbon --subject sub-DAEK --h emi lh

Output: Number of labels: 0 Annot File: ../lh.yeo2011.annot Template Volume: (null) Outut Volume: lh.yeo2011_in_nat.mgz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: sub-DAEK Hemi: lh UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects 7.2.0 INFO: loading surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.white nvertices = 253237 Reading thickness /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.thickness Loading annotations from ../lh.yeo2011.annot annotidmax = 48 nlabels = 48 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgz Mapping Segmentation fault

----Same thing occurs for the right hemi

On Wed, Jun 22, 2022 at 11:42 AM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,

Do you mean the issue that ‘mri_label2vol –fill-ribbon’ crashes? Can you re-run and provide your mris_label2annot and mri_label2vol command line and output?

I’m not sure I will be able to offer work around, but I would like to understand the problem better for future development.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Tuesday, June 21, 2022 5:04 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

It seems that this did not solve the issue. Are there any other reasons why this would occur?

Ben

On Fri, Jun 17, 2022 at 2:59 PM Benjamin Deck <bdeck8317@gmail.commailto:bdeck8317@gmail.com> wrote: Hi Yujing,

Thank you. I will give it a try! Can documentation be updated?

Ben

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On Fri, Jun 17, 2022 at 2:56 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,

Just wanted to update you on mris_label2annot command line options.

If ‘--no-unknown’ is used with mris_label2annot, ‘—offset 1’ should also be specified.

Yujing

From: Huang, Yujing Sent: Thursday, June 16, 2022 1:59 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: RE: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

Hi Ben,

I’m learning it myself too.

I played it a little more. I see the mismatch can happen if you skip a number in you LUT.

Also, if you have ‘0 Unknown 0 0 0 0’ in your LUT, I’m not sure you should use ‘--no-unknown’ for mris_label2annot. It will cause your annotation off by one.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Thursday, June 16, 2022 10:58 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

Thanks for taking a look. What do you mean by mismatch?

The LUT was used to make the annot file. What would generate this mismatch?

Here is the output from my mris_label2annot call:

mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --hemi lh Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 105 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 1 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_10_ROIs_1_lh_native.label 2 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_11_ROIs_1_lh_native.label 3 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_1_lh_native.label 4 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_2_lh_native.label 5 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_1_lh_native.label 6 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_2_lh_native.label 7 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_3_lh_native.label 8 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_4_lh_native.label 9 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_5_lh_native.label 10 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_1_lh_native.label 11 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_2_lh_native.label 12 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_3_lh_native.label 13 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_4_lh_native.label 14 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_5_lh_native.label 15 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_15_ROIs_1_lh_native.label 16 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_1_lh_native.label 17 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_2_lh_native.label 18 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_1_lh_native.label 19 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_2_lh_native.label 20 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_3_lh_native.label 21 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_4_lh_native.label 22 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_1_lh_native.label 23 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_2_lh_native.label 24 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_3_lh_native.label 25 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_4_lh_native.label 26 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_5_lh_native.label 27 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_19_ROIs_1_lh_native.label 28 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_1_lh_native.label 29 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_2_lh_native.label 30 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_1_lh_native.label 31 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_2_lh_native.label 32 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_3_lh_native.label 33 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_4_ROIs_1_lh_native.label 34 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_1_lh_native.label 35 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_2_lh_native.label 36 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_3_lh_native.label 37 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_4_lh_native.label 38 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_1_lh_native.label 39 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_2_lh_native.label 40 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_3_lh_native.label 41 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_1_lh_native.label 42 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_2_lh_native.label 43 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_1_lh_native.label 44 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_2_lh_native.label 45 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_3_lh_native.label 46 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_4_lh_native.label 47 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_5_lh_native.label 48 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_1_lh_native.label 49 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_2_lh_native.label 50 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_3_lh_native.label

7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --hemi lh sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 50 LabelThresh 0 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig 0 1336330 Net_10_ROIs_1_lh_native 1 1639705 Net_11_ROIs_1_lh_native 2 2647065 Net_12_ROIs_1_lh_native 3 11829830 Net_12_ROIs_2_lh_native 4 25700 Net_13_ROIs_1_lh_native 5 16399044 Net_13_ROIs_2_lh_native 6 6500 Net_13_ROIs_3_lh_native 7 3294840 Net_13_ROIs_4_lh_native 8 660700 Net_13_ROIs_5_lh_native 9 6558940 Net_14_ROIs_1_lh_native 10 7874740 Net_14_ROIs_2_lh_native 11 14465658 Net_14_ROIs_3_lh_native 12 9180300 Net_14_ROIs_4_lh_native 13 12300 Net_14_ROIs_5_lh_native 14 9182740 Net_15_ROIs_1_lh_native 15 3296035 Net_16_ROIs_1_lh_native 16 9211105 Net_16_ROIs_2_lh_native 17 4924360 Net_17_ROIs_1_lh_native 18 3302560 Net_17_ROIs_2_lh_native 19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native 21 13777468 Net_18_ROIs_1_lh_native 22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native 24 3294765 Net_18_ROIs_4_lh_native 25 14443610 Net_18_ROIs_5_lh_native 26 10511400 Net_19_ROIs_1_lh_native 27 8323072 Net_2_ROIs_1_lh_native 28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native 30 1316060 Net_3_ROIs_2_lh_native 31 14464220 Net_3_ROIs_3_lh_native 32 8323072 Net_4_ROIs_1_lh_native 33 7874740 Net_5_ROIs_1_lh_native 34 9180300 Net_5_ROIs_2_lh_native 35 8860211 Net_5_ROIs_3_lh_native 36 9182740 Net_5_ROIs_4_lh_native 37 3296035 Net_6_ROIs_1_lh_native 38 9211105 Net_6_ROIs_2_lh_native 39 4924360 Net_6_ROIs_3_lh_native 40 3302560 Net_7_ROIs_1_lh_native 41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native 45 3302620 Net_8_ROIs_4_lh_native 46 10811612 Net_8_ROIs_5_lh_native 47 2637020 Net_9_ROIs_1_lh_native 48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot

Thanks,

Ben

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On Tue, Jun 14, 2022 at 1:33 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,

I was able to reproduce the core dump. In my case, it was because a mismatch of color scheme between input annotation file and the color table loaded with the surface.

I suspect it might be the same issue for you too. But I’m not sure what the right action is to work around this.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Friday, June 10, 2022 11:47 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi there,

Having issues with the following command:

mri_label2vol --annot lh.yeo_2011.annot --temp /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz --hemi lh --fill-ribbon --identity --subject sub-DAEK --o lh.sub-DAEK_annot_nat.nii.gz

produces the following error:

Number of labels: 0 Annot File: lh.yeo_2011.annot Template Volume: /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz Outut Volume: lh.sub-DAEK_annot_nat.nii.gz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: sub-DAEK Hemi: lh UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects 7.2.0 Template RAS-to-Vox: -------- -1.25000 -0.00000 -0.00000 160.00000; -0.00000 -0.00000 -1.25000 160.00000; -0.00000 1.25000 -0.00000 160.00000; -0.00000 -0.00000 -0.00000 1.00000; Template Voxel Volume: 0.512 nHits Thresh: 0 Using Identity Matrix RegMat: -------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Label RAS-to-Vox: -------- -1.25000 0.00000 0.00000 160.00000; 0.00000 0.00000 -1.25000 160.00000; 0.00000 1.25000 0.00000 160.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.white nvertices = 253237 Reading thickness /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.thickness Loading annotations from lh.yeo_2011.annot annotidmax = 48 nlabels = 48 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgz Mapping Segmentation fault

But when I run the same command without fill-ribbon the process runs to completion.

Not sure if this is a memory issue or something else.

Ben

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University

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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1FUT55eeYf35M-JkMc7UcSX6tQwoolQhFqBp-8LICAUTK0wswJKgW_N0VLBuD8TraBJXxv3A6xEtjOi3zHO6u6hS8qtjCvZLT8blEvNFm05eSJH6b8e3aKqHBqbtFAVOULtn9jgTodt8mPW8m3GmSRUmYpxpu9C3Fkzsso7QpJnn8ogCvZ1glcbo1qzY7f0tbdno7w-kyEgSnfbCNbMMoMyfrKVBy_uY9PmTLYP1fcwc9XbQsn81kFW3GvhlFpwBGRN3Le_la1zqvtr5WRJXwA7glAv3TYsHu2WOT_uygJjXNbYUcMNoxCuIb_tjOc9SD/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/129Kw4R0yoVeTC6bBd1uPUqKUYuQfV-mbD5MR0g-xyo9r99gu2Z-4tY7718A6CVUVsK1u7S1awCDro02sozDsoDFvIHYrhSD5vMlHw_EqisjHZyR11ZdEG2yXwgzu8-sfddrPtz3WvbkujxTvALD-PjFOcUYI_NvZuv-09oniwNIjtKWtpQ32jhSYbp70bpRYQbXH0r71ZqTKS8pYf708p8tjI23a7uEnlutWE573EHFSyZ96N8DYzjiawb99BHqVBLAHIt9CDL5wOEykkXYkYd_eyC6CASQ3k0otyq32qfMyZs0UoWTGjs1OtVTWvtUe/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/129Kw4R0yoVeTC6bBd1uPUqKUYuQfV-mbD5MR0g-xyo9r99gu2Z-4tY7718A6CVUVsK1u7S1awCDro02sozDsoDFvIHYrhSD5vMlHw_EqisjHZyR11ZdEG2yXwgzu8-sfddrPtz3WvbkujxTvALD-PjFOcUYI_NvZuv-09oniwNIjtKWtpQ32jhSYbp70bpRYQbXH0r71ZqTKS8pYf708p8tjI23a7uEnlutWE573EHFSyZ96N8DYzjiawb99BHqVBLAHIt9CDL5wOEykkXYkYd_eyC6CASQ3k0otyq32qfMyZs0UoWTGjs1OtVTWvtUe/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1KFYgeucywv-sgvlszrUVmMExT1D1wTosDU5A-ke32OnzTiJE16BPNnIWUUrRFHCfQlcwzvjB9Q_K1vkrSEJCUQDTLqRHU2UEQjr1vhUytcvG7hKX9glUJjoxbSUY8O_1bQYvpZ7TOKLJ9YXI87fsdsCjOCH8pB3fiIxiezlWu0z6nZe6wVVSJFDrDdBem0x4EW9r5DDygdavp_pb5Y0W7eDFR-iX1WCGnPMNjDjpXexXTIdI_Ol2eLqKWFGHW4MUrUqdaqwYDldwTkGvUFz36lUI7bBBSR8z1QvvqnzPopmvsUdYFcp1-fYYTK9hnrhV/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1KBqYHmYqf-cm-adopQpa1hFDYwc2XxJdOhqXuwG4-p6H_zGJt9CzUb5Bcvty-89vJmkrh4_Y832uL8-DrSaORXDjxvEkwEs8RtxEuQq6lUEUmTfDzlsSL76rkunUEu1FsCKZ4XZ2Wo3E5uXvAb9ZbgagP66-F2BJ-VUqW_2K-K6ArkhyxeOBbFK_7nQsQrvVhi-lxaWl99ahxDwxvyDw0a4G2bKYecYvPx4JDXZOIqOnUJXhrMxb6r-ORsKccILBkvac-C0TUvVDohtWjtbk5SAJgnuIecC_IkYNBNjmdIGPIAtOk50-zSkafZunnfTb/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1KBqYHmYqf-cm-adopQpa1hFDYwc2XxJdOhqXuwG4-p6H_zGJt9CzUb5Bcvty-89vJmkrh4_Y832uL8-DrSaORXDjxvEkwEs8RtxEuQq6lUEUmTfDzlsSL76rkunUEu1FsCKZ4XZ2Wo3E5uXvAb9ZbgagP66-F2BJ-VUqW_2K-K6ArkhyxeOBbFK_7nQsQrvVhi-lxaWl99ahxDwxvyDw0a4G2bKYecYvPx4JDXZOIqOnUJXhrMxb6r-ORsKccILBkvac-C0TUvVDohtWjtbk5SAJgnuIecC_IkYNBNjmdIGPIAtOk50-zSkafZunnfTb/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1pg-D_wLryyZksJTKvQ2XCj2jB5SkB2H8DVHgj5FtQzPyNkniuHdTaL_IBFsxabyNQVwyDAGRDb0cGEIzTIwtcuvIjwV3Lg7QiLDyCU74wL7e7OWYfCCCREmXi9pTrSNypqR7dIGxdS9SqZWfBT2kNZZz3MP8T3iMaDPJB9tUGA0ftI51Y1MpTzJb0BuB7LpTw9riLUlNPvZd3ibg1m7sC629TtuUgdOT-UbH-LxXKgxPhoGJTq0JLzVzIVxqiHbwMlHBsuO84niKNg6mU818Tct_f3UyRX5FTrDYdFHzIsp8PP-5erbf9ISg_MOJtcBAuHtG9F7ocoXiqQITXSSQuw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1ewws5jb1hRDkswPgWMqJP5exouHEKg_qKAlpTyoWlL_21LVGF-OMt6D7Slbg57sQbZwXOVLoDnC9YmdlJJzCPz_HQflF5OSUSoOzRFqBb6S3Zj7jBeo3gp2dpeZTH5IAbvwMwJpAhQONN1708QcTAGvm0HQozK-hXCPgp3gdbe5lVhSGPdR8e1sEZJXq-rZdgdTLIf1a_-e1YvYd5r2ev1HhSuWmyQ5RsQA7Bcb_Rh2TEkdyOmIr0twh52ig6Lrx-_i0r-cciGHcHqmJL_nfrTjOePOVj-htPLFiL1A6BFbEZOUR5-kiUNSZMT9PrStO3fWQUbb7X1WIRA8SBCJQXg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1ewws5jb1hRDkswPgWMqJP5exouHEKg_qKAlpTyoWlL_21LVGF-OMt6D7Slbg57sQbZwXOVLoDnC9YmdlJJzCPz_HQflF5OSUSoOzRFqBb6S3Zj7jBeo3gp2dpeZTH5IAbvwMwJpAhQONN1708QcTAGvm0HQozK-hXCPgp3gdbe5lVhSGPdR8e1sEZJXq-rZdgdTLIf1a_-e1YvYd5r2ev1HhSuWmyQ5RsQA7Bcb_Rh2TEkdyOmIr0twh52ig6Lrx-_i0r-cciGHcHqmJL_nfrTjOePOVj-htPLFiL1A6BFbEZOUR5-kiUNSZMT9PrStO3fWQUbb7X1WIRA8SBCJQXg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1ohxFwDlj95GLWi92_zXWezKzkZSexk4R2BjNZnepB4disZNNuSpW1kK96h-7gzHWzHAfWDFB-dq5WFtrzogG_IDQxfKJM9_8THWm2gTlYr7E4JMzy50EQ0biIxFBc18A7TnYbRKYCW423M2Et_XUa845uEAbuqGRY-rPn8VINSo8n-KcLzZVfZIDWMcJfZiUh7nY6YlsjtlsatA_dXwilbQbksrtIoKDz9rGY5xmZZBLw_VbP8y8YHRyqOrPg4z8ic10lMUnmQgTlmAQ2YgWJ1xKBUPxs5Yk4ek3dLoLkM-g8rkKGlnK7y8aIl9YsPhk/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1gWC8FomBEWvS9SwG5Wk_5Npjvbjt5_29f_qSVE6r4gTYuQr1OZ3heuVWDhm6ygbJNNjl1rcmbLynrODhMW7zGVFOVKJuo9VGT_6ZzY4tD4lpW48h_e3rKiASiRE6iSmhswYQZU3h8c7vDBMokS0is2ROd2vxRcBpVk8R4coPUJm4HAxL7IJkyp9T1IOseEkAQ6Evmgof8igvqcLT9jVdvH6LXAARWQN8TW7ZoIwVtabTajMFOgP-2A0Kg_EmGcDvJqIrVwP2p0e0olstkbXWUkMW1IkROWarolKJ4h73QIjEXEmYKXqsMD_PaNG0quCB/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1gWC8FomBEWvS9SwG5Wk_5Npjvbjt5_29f_qSVE6r4gTYuQr1OZ3heuVWDhm6ygbJNNjl1rcmbLynrODhMW7zGVFOVKJuo9VGT_6ZzY4tD4lpW48h_e3rKiASiRE6iSmhswYQZU3h8c7vDBMokS0is2ROd2vxRcBpVk8R4coPUJm4HAxL7IJkyp9T1IOseEkAQ6Evmgof8igvqcLT9jVdvH6LXAARWQN8TW7ZoIwVtabTajMFOgP-2A0Kg_EmGcDvJqIrVwP2p0e0olstkbXWUkMW1IkROWarolKJ4h73QIjEXEmYKXqsMD_PaNG0quCB/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1-Co0Tj3nO9PKVc4FF5EYp-pbwW1MSBhpVRo4lPgCIr_Le-jinRghImfaUz1XwH3bS9-3JJtGF7iqyCINnenimFyLBFGtPvkx4gKT4LM_XuqtA8yehAilreaW-7tfG7rFm9CKmyvL6UTMUL8ixh3tIeZDVlTa-WL09UQo8OB3xQPLEOyeBBTdvYOD9-EejJcMmPhvCbVyM7VATQc4WnF3BT3C9Wr5Fp2UY25cbOG0IiS9S3TID8jUqddMj_O_8SHKh8odIuW_MNbPu35lVuaMTi9Gh9V0u7p3tOIkH4vOTMN-8GTlTCP5safglQWXvSSt/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1nUKsaivbAuxJojvr0yFs7hY0LXQON0_HrlCUPtW5ymN-QLI0xMSE64vbmxo74tTH5VaFyluU46uvw3l-Oi9Zs6J_C9ApmKC6YBCM7Vp9dxkgV2G-JQiYfsxps_neYqUYs3Ex6cqTkpvxd29lBZXFfOAAEuEh89KJ9t3RbBTeOlzXr_mxGPrA9_wXx5Ik_NMVLgPT_qhUj3n03BUZBWoYAS8fR1HG-dDJAvMSNEIbB4DEEaIO1w4toFS_NkYAtb0_kF5ch2aEyPtKeAXZXAQNHORaUhvK4OmoxzwZuVrxEFBj3kjicTmAplnxy8Ns7pjx/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1nUKsaivbAuxJojvr0yFs7hY0LXQON0_HrlCUPtW5ymN-QLI0xMSE64vbmxo74tTH5VaFyluU46uvw3l-Oi9Zs6J_C9ApmKC6YBCM7Vp9dxkgV2G-JQiYfsxps_neYqUYs3Ex6cqTkpvxd29lBZXFfOAAEuEh89KJ9t3RbBTeOlzXr_mxGPrA9_wXx5Ik_NMVLgPT_qhUj3n03BUZBWoYAS8fR1HG-dDJAvMSNEIbB4DEEaIO1w4toFS_NkYAtb0_kF5ch2aEyPtKeAXZXAQNHORaUhvK4OmoxzwZuVrxEFBj3kjicTmAplnxy8Ns7pjx/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1vY_16Zjww2xu0uzWyiUohSSGGRD2H3nPfBx-WboNIK-KoK15rtSqkX2N-vmZ_cZ27ff2CpMOXLf512LEyZ_evkkY3h5Fj3fd8kZmWMbNzbz13qEX-J_IC_P6asO8e2VQ_smAoIOlIkFkOJHjdqGr04XT2bVWuPZjC9dOlUH26F47LauKhAEPdxCKLr4NE9Pv3ivq0eZZ5kFH0bqLzGyz0nNRpBvXgkwvnlq8hqiHZ8Bxe0h2o9TE0GEYSMPGRmj3BKHyBYVGLsX58dmumT-cSW8AEvkCb91oK2Lv-DywOJBySAA4UnwaUtsPVsa-Qaz80DhUEKpRssMKaD0KwpO1-Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1KyPIPmRNwus-z79lEGn0T7diD2lNJqoI2KIQh4lMv2faOIlvJOXCKLsN35WtRkxw61rareTh_XeaqS274mShL_BwFF0zrupuNsCOKEU94cyu7wYoAM6A93LTuYfY69rB1_3laFePNZaecZtHzcaAqoooOI2HEKJu89TZc6ronKly_Y7oIPveyaULOt3u4wFYCT2PowbhyLRJ5rEfGIkGksjlIxIB46ynWAQuDbi1KJPj7YPc039Tros_bYxNL_UjuGzrk_VVjobmcicqBvJbHh69MPWijPmHDSLTSx76IPcDo85-lkMmm_-3yhZXEoMMFwMXN-kGs8rg9zY0wYgyNQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1KyPIPmRNwus-z79lEGn0T7diD2lNJqoI2KIQh4lMv2faOIlvJOXCKLsN35WtRkxw61rareTh_XeaqS274mShL_BwFF0zrupuNsCOKEU94cyu7wYoAM6A93LTuYfY69rB1_3laFePNZaecZtHzcaAqoooOI2HEKJu89TZc6ronKly_Y7oIPveyaULOt3u4wFYCT2PowbhyLRJ5rEfGIkGksjlIxIB46ynWAQuDbi1KJPj7YPc039Tros_bYxNL_UjuGzrk_VVjobmcicqBvJbHh69MPWijPmHDSLTSx76IPcDo85-lkMmm_-3yhZXEoMMFwMXN-kGs8rg9zY0wYgyNQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University

Hi Ben,

Sorry for all the troubles.

I’m trying to reproduce here. I found aparc.annot.ctab in bert directory. I have a question about the label files. Are they part of the tutorial data? Where did you download the data? I don’t see those label files in the directory.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Benjamin Deck Sent: Sunday, June 26, 2022 3:02 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution So I thought that since this has caused me many issues I would test this on the bert subject using aparc.annot. These are default with freesurfer.

command using Bert: cwd /mnt/c/Users/Ben/freesurfer/subjects/bert/label cmdline mris_label2annot --s bert --hemi lh --ctab /mnt/c/Users/Ben/freesurfer/subjects/bert/label/aparc.annot.ctab --a myaparc --ldir /mnt/c/Users/Ben/freesurfer/subjects/bert/label/ sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject bert hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable /mnt/c/Users/Ben/freesurfer/subjects/bert/label/aparc.annot.ctab AnnotName myaparc nlables 35 LabelThresh 0 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/bert/surf/lh.orig 1 2647065 bankssts 2 10511485 caudalanteriorcingulate 3 6500 caudalmiddlefrontal 4 6558940 cuneus 5 660700 entorhinal 6 9231540 fusiform 7 14433500 inferiorparietal 8 7874740 inferiortemporal 9 9180300 isthmuscingulate 10 9182740 lateraloccipital 11 3296035 lateralorbitofrontal 12 9211105 lingual 13 4924360 medialorbitofrontal 14 3302560 middletemporal 15 3988500 parahippocampal 16 3988540 paracentral 17 9221340 parsopercularis 18 3302420 parsorbitalis 19 1326300 parstriangularis 20 3957880 pericalcarine 21 1316060 postcentral 22 14464220 posteriorcingulate 23 14423100 precentral 24 11832480 precuneus 25 9180240 rostralanteriorcingulate 26 8204875 rostralmiddlefrontal 27 10542100 superiorfrontal 28 9221140 superiorparietal 29 14474380 superiortemporal 30 1351760 supramarginal 31 6553700 frontalpole 32 11146310 temporalpole 33 13145750 transversetemporal 34 2146559 insula 35 11223921 cluster35 Mapping unhit to unknown Found 0 unhit vertices Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/bert/label/lh.myaparc.annot _____________________________________________________________________

It seems to be not indexing properly into the CTAB file

CTAB:

0 unknown 25 5 25 0 1 bankssts 25 100 40 0 2 caudalanteriorcingulate 125 100 160 0 3 caudalmiddlefrontal 100 25 0 0 4 corpuscallosum 120 70 50 0 5 cuneus 220 20 100 0 6 entorhinal 220 20 10 0 7 fusiform 180 220 140 0 8 inferiorparietal 220 60 220 0 9 inferiortemporal 180 40 120 0 10 isthmuscingulate 140 20 140 0 11 lateraloccipital 20 30 140 0 12 lateralorbitofrontal 35 75 50 0 13 lingual 225 140 140 0 14 medialorbitofrontal 200 35 75 0 15 middletemporal 160 100 50 0 16 parahippocampal 20 220 60 0 17 paracentral 60 220 60 0 18 parsopercularis 220 180 140 0 19 parsorbitalis 20 100 50 0 20 parstriangularis 220 60 20 0 21 pericalcarine 120 100 60 0 22 postcentral 220 20 20 0 23 posteriorcingulate 220 180 220 0 24 precentral 60 20 220 0 25 precuneus 160 140 180 0 26 rostralanteriorcingulate 80 20 140 0 27 rostralmiddlefrontal 75 50 125 0 28 superiorfrontal 20 220 160 0 29 superiorparietal 20 180 140 0 30 superiortemporal 140 220 220 0 31 supramarginal 80 160 20 0 32 frontalpole 100 0 100 0 33 temporalpole 70 20 170 0 34 transversetemporal 150 150 200 0 35 insula 255 192 32 0

I really have no idea why it returns this nondescript cluster 35--- there shouldn't be a cluster 35.

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On Fri, Jun 24, 2022 at 5:10 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: I noticed two things: 1. you have skipped numbers in label files output - make sure all label names in LUT have corresponding label files hemi.label-name.label in ldir directory. 2. your annotation output doesn’t agree with the LUT your showed - make sure you are passing the correct copy to mris_label2annot

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Friday, June 24, 2022 4:47 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

I just re-ran this and I am now noticing something else that is strange.

I included an "unknown 0 0 0 0" row at the beginning and gave this a 0 index. Similar to the default LUT

LUT: 0 Unknown 255 255 255 0 1 Net_14_ROIs_4_native 25 5 25 0 2 Net_9_ROIs_1_native 25 100 40 0 3 Net_18_ROIs_4_native 70 130 180 0

My command and output:

mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --ctab sub-DAEK_yeoLUT.txt --maxstatwinner --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019/ Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 57 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 1 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_14_ROIs_4_native.label 2 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_9_ROIs_1_native.label 3 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_18_ROIs_4_native.label 4 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_8_ROIs_1_native.label 5 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_14_ROIs_1_native.label 7 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_14_ROIs_2_native.label 8 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_6_ROIs_1_native.label 10 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_9_ROIs_2_native.label 11 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_8_ROIs_3_native.label 12 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_17_ROIs_3_native.label 13 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_10_ROIs_1_native.label 14 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_5_ROIs_3_native.label 15 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_16_ROIs_2_native.label 16 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_5_ROIs_4_native.label 17 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_9_ROIs_3_native.label 18 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_18_ROIs_3_native.label 20 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_13_ROIs_2_native.label 21 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_2_ROIs_1_native.label 23 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_5_ROIs_1_native.label 24 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_13_ROIs_1_native.label 25 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_8_ROIs_4_native.label 26 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_13_ROIs_3_native.label 27 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_8_ROIs_2_native.label 28 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_18_ROIs_5_native.label 29 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_17_ROIs_2_native.label 30 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_12_ROIs_1_native.label 31 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_3_ROIs_3_native.label 32 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_18_ROIs_1_native.label 33 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_11_ROIs_1_native.label 35 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_3_ROIs_2_native.label 36 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_6_ROIs_2_native.label 37 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_13_ROIs_4_native.label 39 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_15_ROIs_1_native.label 40 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_7_ROIs_1_native.label 41 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_18_ROIs_2_native.label 42 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_19_ROIs_1_native.label 43 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_2_ROIs_2_native.label 44 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_5_ROIs_2_native.label 45 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_16_ROIs_1_native.label 46 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_14_ROIs_5_native.label 47 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_13_ROIs_5_native.label 48 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_3_ROIs_1_native.label 49 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_7_ROIs_2_native.label 50 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_12_ROIs_2_native.label 51 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_8_ROIs_5_native.label 52 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_17_ROIs_4_native.label 53 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_4_ROIs_1_native.label 54 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_17_ROIs_1_native.label 55 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_14_ROIs_3_native.label 56 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_6_ROIs_3_native.label

7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019 cmdline mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --ctab sub-DAEK_yeoLUT.txt --maxstatwinner --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019/ sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 50 LabelThresh 0 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig 1 2647065 Net_9_ROIs_1_native 2 11829830 Net_18_ROIs_4_native 3 25700 Net_8_ROIs_1_native 4 16399044 Net_14_ROIs_1_native 5 3294840 Net_14_ROIs_2_native 6 660700 Net_6_ROIs_1_native 7 7874740 Net_9_ROIs_2_native 8 14465658 Net_8_ROIs_3_native 9 9180300 Net_17_ROIs_3_native 10 12300 Net_10_ROIs_1_native 11 9182740 Net_5_ROIs_3_native 12 3296035 Net_16_ROIs_2_native 13 9211105 Net_5_ROIs_4_native 14 4924360 Net_9_ROIs_3_native 15 3302560 Net_18_ROIs_3_native 16 3988540 Net_13_ROIs_2_native 17 13777468 Net_2_ROIs_1_native 18 3302420 Net_5_ROIs_1_native 19 3294765 Net_13_ROIs_1_native 20 14443610 Net_8_ROIs_4_native 21 10511400 Net_13_ROIs_3_native 22 8323072 Net_8_ROIs_2_native 23 1326300 Net_18_ROIs_5_native 24 3957880 Net_17_ROIs_2_native 25 1316060 Net_12_ROIs_1_native 26 14464220 Net_3_ROIs_3_native 27 8323072 Net_18_ROIs_1_native 28 7874740 Net_11_ROIs_1_native 29 8860211 Net_3_ROIs_2_native 30 9182740 Net_6_ROIs_2_native 31 3296035 Net_13_ROIs_4_native 32 4924360 Net_15_ROIs_1_native 33 3302560 Net_7_ROIs_1_native 34 3988500 Net_18_ROIs_2_native 35 3988540 Net_19_ROIs_1_native 36 9221340 Net_2_ROIs_2_native 37 3302420 Net_5_ROIs_2_native 38 3302620 Net_16_ROIs_1_native 39 10811612 Net_14_ROIs_5_native 40 2637020 Net_13_ROIs_5_native 41 1326300 Net_3_ROIs_1_native 42 3957880 Net_7_ROIs_2_native 43 1316060 Net_12_ROIs_2_native 44 14464220 Net_8_ROIs_5_native 45 14423100 Net_17_ROIs_4_native 46 11832480 Net_4_ROIs_1_native 47 9180240 Net_17_ROIs_1_native 48 8204875 Net_14_ROIs_3_native 49 10542100 Net_6_ROIs_3_native 50 3840729 cluster50 Mapping unhit to unknown Found 19023 unhit vertices Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot

For some very weird reason it skips my 0 row, 'unknown' and then adds an undescript cluster at the end.

Why is that occurring?

Ben

On Fri, Jun 24, 2022 at 4:00 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,

Based on your command line options (‘—no-unknown –offset 0’) and output, I believe your LUT starts with ‘0 Net_10_ROIs_1_lh_native 255 255 255 0’ not ‘0 Unknown 0 0 0 0’. Can you double check the LUT you passed to mris_label2annot?

I was able to reproduce the crash with duplicated color scheme scenario. Once you fix duplicated color schemes in your LUT, ‘mris_label2vol –fill-ribbon’ should run fine.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Thursday, June 23, 2022 10:42 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hmm.. I see what you're saying not the names but the actual location. Shouldn't I be getting a warning of overlapping labels and therefore an arg like --maxstatwinner would be helpful?

On Thu, Jun 23, 2022 at 10:34 AM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: For the duplicates, 19 is same as 41, 20 is same as 42, …

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Thursday, June 23, 2022 10:27 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

Thanks for your continued support on this issue.

Addressing your first question.

If I use --offset 1 then the get the following:

cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --offset 1 sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 50 LabelThresh 1 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig 1 1639705 Net_11_ROIs_1_lh_native 2 2647065 Net_12_ROIs_1_lh_native 3 11829830 Net_12_ROIs_2_lh_native 4 25700 Net_13_ROIs_1_lh_native 5 16399044 Net_13_ROIs_2_lh_native 6 6500 Net_13_ROIs_3_lh_native 7 3294840 Net_13_ROIs_4_lh_native 8 660700 Net_13_ROIs_5_lh_native 9 6558940 Net_14_ROIs_1_lh_native 10 7874740 Net_14_ROIs_2_lh_native 11 14465658 Net_14_ROIs_3_lh_native 12 9180300 Net_14_ROIs_4_lh_native 13 12300 Net_14_ROIs_5_lh_native 14 9182740 Net_15_ROIs_1_lh_native 15 3296035 Net_16_ROIs_1_lh_native 16 9211105 Net_16_ROIs_2_lh_native 17 4924360 Net_17_ROIs_1_lh_native 18 3302560 Net_17_ROIs_2_lh_native 19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native 21 13777468 Net_18_ROIs_1_lh_native 22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native 24 3294765 Net_18_ROIs_4_lh_native 25 14443610 Net_18_ROIs_5_lh_native 26 10511400 Net_19_ROIs_1_lh_native 27 8323072 Net_2_ROIs_1_lh_native 28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native 30 1316060 Net_3_ROIs_2_lh_native 31 14464220 Net_3_ROIs_3_lh_native 32 8323072 Net_4_ROIs_1_lh_native 33 7874740 Net_5_ROIs_1_lh_native 34 9180300 Net_5_ROIs_2_lh_native 35 8860211 Net_5_ROIs_3_lh_native 36 9182740 Net_5_ROIs_4_lh_native 37 3296035 Net_6_ROIs_1_lh_native 38 9211105 Net_6_ROIs_2_lh_native 39 4924360 Net_6_ROIs_3_lh_native 40 3302560 Net_7_ROIs_1_lh_native 41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native 45 3302620 Net_8_ROIs_4_lh_native 46 10811612 Net_8_ROIs_5_lh_native 47 2637020 Net_9_ROIs_1_lh_native 48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native 50 791413 cluster50 Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot

Where cluster50 is some nondescript cluster and it ignores my network 10 which should be the first entry.

To address your second question about duplicates.

19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native

While these may look almost like duplicates they are different rois within the same larger network. This separation is important for what I am doing so I need to keep the ROIs separate from one another but they are a part of the same larger network. However, Freesurfer doesn't know that they are.

On Thu, Jun 23, 2022 at 10:17 AM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: I am confused about ‘—no-unknown –offset 0’. Your output doesn’t seem agree with the codes. If your label starts at 1, I think it should be ‘—offset 1’ instead of 0. Can you double check your LUT?

I see duplicates in second column of these lines: (second column is calculated from RGB values.)

19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native

22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native

28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native

41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native

48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Thursday, June 23, 2022 9:36 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

I am not seeing any duplicates--highlighting wasn't rendered on my end.

my LUT:

0 Unknown 0 0 0 0 1 Net_10_ROIs_1_lh_native 255 255 255 0 2 Net_11_ROIs_1_lh_native 25 5 25 0 3 Net_12_ROIs_1_lh_native 25 100 40 0 4 Net_12_ROIs_2_lh_native 70 130 180 0 5 Net_13_ROIs_1_lh_native 100 100 0 0 6 Net_13_ROIs_2_lh_native 196 58 250 0

which is why I gave the --offset flag as 0 for --no-unknown

I did notice that the labels is incorrect. So for some reason, it seems to be missing two labels that exist in the annotation. That is strange.

Ben

On Thu, Jun 23, 2022 at 8:55 AM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: How does your LUT look like? What is your first line?

For left hemi, your loaded 50 label files to mris_label2annot, but mri_label2vol only reported 48 labels. It looks like you have duplicated RGB in your LUT. I have identified some. See highlighted in red. The duplicated RGB entries can cause problems.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Wednesday, June 22, 2022 2:24 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

Sure thing.

Commands:

mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt

Output: Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 105 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 1 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_10_ROIs_1_lh_native.label 2 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_11_ROIs_1_lh_native.label 3 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_1_lh_native.label 4 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_2_lh_native.label 5 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_1_lh_native.label 6 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_2_lh_native.label 7 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_3_lh_native.label 8 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_4_lh_native.label 9 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_5_lh_native.label 10 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_1_lh_native.label 11 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_2_lh_native.label 12 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_3_lh_native.label 13 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_4_lh_native.label 14 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_5_lh_native.label 15 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_15_ROIs_1_lh_native.label 16 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_1_lh_native.label 17 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_2_lh_native.label 18 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_1_lh_native.label 19 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_2_lh_native.label 20 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_3_lh_native.label 21 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_4_lh_native.label 22 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_1_lh_native.label 23 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_2_lh_native.label 24 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_3_lh_native.label 25 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_4_lh_native.label 26 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_5_lh_native.label 27 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_19_ROIs_1_lh_native.label 28 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_1_lh_native.label 29 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_2_lh_native.label 30 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_1_lh_native.label 31 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_2_lh_native.label 32 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_3_lh_native.label 33 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_4_ROIs_1_lh_native.label 34 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_1_lh_native.label 35 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_2_lh_native.label 36 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_3_lh_native.label 37 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_4_lh_native.label 38 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_1_lh_native.label 39 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_2_lh_native.label 40 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_3_lh_native.label 41 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_1_lh_native.label 42 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_2_lh_native.label 43 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_1_lh_native.label 44 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_2_lh_native.label 45 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_3_lh_native.label 46 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_4_lh_native.label 47 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_5_lh_native.label 48 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_1_lh_native.label 49 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_2_lh_native.label 50 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_3_lh_native.label

7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 50 LabelThresh 1 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig 0 16777215 Net_10_ROIs_1_lh_native 1 1639705 Net_11_ROIs_1_lh_native 2 2647065 Net_12_ROIs_1_lh_native 3 11829830 Net_12_ROIs_2_lh_native 4 25700 Net_13_ROIs_1_lh_native 5 16399044 Net_13_ROIs_2_lh_native 6 6500 Net_13_ROIs_3_lh_native 7 3294840 Net_13_ROIs_4_lh_native 8 660700 Net_13_ROIs_5_lh_native 9 6558940 Net_14_ROIs_1_lh_native 10 7874740 Net_14_ROIs_2_lh_native 11 14465658 Net_14_ROIs_3_lh_native 12 9180300 Net_14_ROIs_4_lh_native 13 12300 Net_14_ROIs_5_lh_native 14 9182740 Net_15_ROIs_1_lh_native 15 3296035 Net_16_ROIs_1_lh_native 16 9211105 Net_16_ROIs_2_lh_native 17 4924360 Net_17_ROIs_1_lh_native 18 3302560 Net_17_ROIs_2_lh_native 19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native 21 13777468 Net_18_ROIs_1_lh_native 22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native 24 3294765 Net_18_ROIs_4_lh_native 25 14443610 Net_18_ROIs_5_lh_native 26 10511400 Net_19_ROIs_1_lh_native 27 8323072 Net_2_ROIs_1_lh_native 28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native 30 1316060 Net_3_ROIs_2_lh_native 31 14464220 Net_3_ROIs_3_lh_native 32 8323072 Net_4_ROIs_1_lh_native 33 7874740 Net_5_ROIs_1_lh_native 34 9180300 Net_5_ROIs_2_lh_native 35 8860211 Net_5_ROIs_3_lh_native 36 9182740 Net_5_ROIs_4_lh_native 37 3296035 Net_6_ROIs_1_lh_native 38 9211105 Net_6_ROIs_2_lh_native 39 4924360 Net_6_ROIs_3_lh_native 40 3302560 Net_7_ROIs_1_lh_native 41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native 45 3302620 Net_8_ROIs_4_lh_native 46 10811612 Net_8_ROIs_5_lh_native 47 2637020 Net_9_ROIs_1_lh_native 48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot

command: mris_label2annot --s sub-DAEK --hemi rh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt

output: Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 105 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 51 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_10_ROIs_1_rh_native.label 52 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_11_ROIs_1_rh_native.label 53 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_12_ROIs_1_rh_native.label 54 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_12_ROIs_2_rh_native.label 55 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_1_rh_native.label 56 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_2_rh_native.label 57 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_3_rh_native.label 58 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_4_rh_native.label 59 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_1_rh_native.label 60 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_2_rh_native.label 61 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_3_rh_native.label 62 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_4_rh_native.label 63 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_5_rh_native.label 64 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_15_ROIs_1_rh_native.label 65 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_1_rh_native.label 66 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_2_rh_native.label 67 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_3_rh_native.label 68 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_1_rh_native.label 69 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_2_rh_native.label 70 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_3_rh_native.label 71 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_4_rh_native.label 72 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_1_rh_native.label 73 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_2_rh_native.label 74 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_3_rh_native.label 75 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_4_rh_native.label 76 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_19_ROIs_1_rh_native.label 77 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_2_ROIs_1_rh_native.label 78 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_2_ROIs_2_rh_native.label 79 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_1_rh_native.label 80 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_2_rh_native.label 81 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_3_rh_native.label 82 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_4_ROIs_1_rh_native.label 83 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_1_rh_native.label 84 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_2_rh_native.label 85 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_3_rh_native.label 86 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_4_rh_native.label 87 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_1_rh_native.label 88 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_2_rh_native.label 89 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_3_rh_native.label 90 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_1_rh_native.label 91 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_2_rh_native.label 92 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_3_rh_native.label 93 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_1_rh_native.label 94 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_2_rh_native.label 95 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_3_rh_native.label 96 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_4_rh_native.label 97 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_5_rh_native.label 98 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_6_rh_native.label 99 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_1_rh_native.label 100 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_2_rh_native.label 101 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_3_rh_native.label 102 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_4_rh_native.label 103 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_5_rh_native.label 104 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_6_rh_native.label

7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --hemi rh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi rh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 54 LabelThresh 1 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/rh.orig 0 1316060 Net_10_ROIs_1_rh_native 1 14464220 Net_11_ROIs_1_rh_native 2 14423100 Net_12_ROIs_1_rh_native 3 11832480 Net_12_ROIs_2_rh_native 4 9180240 Net_13_ROIs_1_rh_native 5 8204875 Net_13_ROIs_2_rh_native 6 10542100 Net_13_ROIs_3_rh_native 7 9231380 Net_13_ROIs_4_rh_native 8 9221140 Net_14_ROIs_1_rh_native 9 14474380 Net_14_ROIs_2_rh_native 10 2763429 Net_14_ROIs_3_rh_native 11 1351760 Net_14_ROIs_4_rh_native 12 15736992 Net_14_ROIs_5_rh_native 13 6553700 Net_15_ROIs_1_rh_native 14 11146310 Net_16_ROIs_1_rh_native 15 13145750 Net_16_ROIs_2_rh_native 16 3311482 Net_16_ROIs_3_rh_native 17 2146304 Net_17_ROIs_1_rh_native 18 5935475 Net_17_ROIs_2_rh_native 19 681085 Net_17_ROIs_3_rh_native 20 23060 Net_17_ROIs_4_rh_native 21 3957760 Net_18_ROIs_1_rh_native 22 3311482 Net_18_ROIs_2_rh_native 23 1321040 Net_18_ROIs_3_rh_native 24 3276922 Net_18_ROIs_4_rh_native 25 6588260 Net_19_ROIs_1_rh_native 26 3957760 Net_2_ROIs_1_rh_native 27 50372 Net_2_ROIs_2_rh_native 28 2671812 Net_3_ROIs_1_rh_native 29 3957956 Net_3_ROIs_2_rh_native 30 6564036 Net_3_ROIs_3_rh_native 31 3945156 Net_4_ROIs_1_rh_native 32 13127690 Net_5_ROIs_1_rh_native 33 6604880 Net_5_ROIs_2_rh_native 34 2647140 Net_5_ROIs_3_rh_native 35 3937480 Net_5_ROIs_4_rh_native 36 665610 Net_6_ROIs_1_rh_native 37 50372 Net_6_ROIs_2_rh_native 38 706590 Net_6_ROIs_3_rh_native 39 5923840 Net_7_ROIs_1_rh_native 40 6579200 Net_7_ROIs_2_rh_native 41 32768 Net_7_ROIs_3_rh_native 42 25600 Net_8_ROIs_1_rh_native 43 13117500 Net_8_ROIs_2_rh_native 44 6574090 Net_8_ROIs_3_rh_native 45 51200 Net_8_ROIs_4_rh_native 46 8320 Net_8_ROIs_5_rh_native 47 25750 Net_8_ROIs_6_rh_native 48 1336330 Net_9_ROIs_1_rh_native 49 25740 Net_9_ROIs_2_rh_native 50 3983360 Net_9_ROIs_3_rh_native 51 7895160 Net_9_ROIs_4_rh_native 52 6553720 Net_9_ROIs_5_rh_native 53 8312 Net_9_ROIs_6_rh_native Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/rh.yeo2011.annot

---Annotations look fine.

Command: mri_label2vol --o lh.yeo2011_in_nat.mgz --annot ../lh.yeo2011.annot --identity --fill-ribbon --subject sub-DAEK --h emi lh

Output: Number of labels: 0 Annot File: ../lh.yeo2011.annot Template Volume: (null) Outut Volume: lh.yeo2011_in_nat.mgz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: sub-DAEK Hemi: lh UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects 7.2.0 INFO: loading surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.white nvertices = 253237 Reading thickness /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.thickness Loading annotations from ../lh.yeo2011.annot annotidmax = 48 nlabels = 48 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgz Mapping Segmentation fault

----Same thing occurs for the right hemi

On Wed, Jun 22, 2022 at 11:42 AM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,

Do you mean the issue that ‘mri_label2vol –fill-ribbon’ crashes? Can you re-run and provide your mris_label2annot and mri_label2vol command line and output?

I’m not sure I will be able to offer work around, but I would like to understand the problem better for future development.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Tuesday, June 21, 2022 5:04 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

It seems that this did not solve the issue. Are there any other reasons why this would occur?

Ben

On Fri, Jun 17, 2022 at 2:59 PM Benjamin Deck <bdeck8317@gmail.commailto:bdeck8317@gmail.com> wrote: Hi Yujing,

Thank you. I will give it a try! Can documentation be updated?

Ben

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On Fri, Jun 17, 2022 at 2:56 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,

Just wanted to update you on mris_label2annot command line options.

If ‘--no-unknown’ is used with mris_label2annot, ‘—offset 1’ should also be specified.

Yujing

From: Huang, Yujing Sent: Thursday, June 16, 2022 1:59 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: RE: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

Hi Ben,

I’m learning it myself too.

I played it a little more. I see the mismatch can happen if you skip a number in you LUT.

Also, if you have ‘0 Unknown 0 0 0 0’ in your LUT, I’m not sure you should use ‘--no-unknown’ for mris_label2annot. It will cause your annotation off by one.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Thursday, June 16, 2022 10:58 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

Thanks for taking a look. What do you mean by mismatch?

The LUT was used to make the annot file. What would generate this mismatch?

Here is the output from my mris_label2annot call:

mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --hemi lh Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 105 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 1 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_10_ROIs_1_lh_native.label 2 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_11_ROIs_1_lh_native.label 3 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_1_lh_native.label 4 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_2_lh_native.label 5 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_1_lh_native.label 6 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_2_lh_native.label 7 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_3_lh_native.label 8 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_4_lh_native.label 9 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_5_lh_native.label 10 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_1_lh_native.label 11 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_2_lh_native.label 12 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_3_lh_native.label 13 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_4_lh_native.label 14 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_5_lh_native.label 15 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_15_ROIs_1_lh_native.label 16 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_1_lh_native.label 17 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_2_lh_native.label 18 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_1_lh_native.label 19 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_2_lh_native.label 20 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_3_lh_native.label 21 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_4_lh_native.label 22 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_1_lh_native.label 23 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_2_lh_native.label 24 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_3_lh_native.label 25 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_4_lh_native.label 26 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_5_lh_native.label 27 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_19_ROIs_1_lh_native.label 28 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_1_lh_native.label 29 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_2_lh_native.label 30 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_1_lh_native.label 31 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_2_lh_native.label 32 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_3_lh_native.label 33 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_4_ROIs_1_lh_native.label 34 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_1_lh_native.label 35 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_2_lh_native.label 36 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_3_lh_native.label 37 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_4_lh_native.label 38 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_1_lh_native.label 39 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_2_lh_native.label 40 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_3_lh_native.label 41 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_1_lh_native.label 42 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_2_lh_native.label 43 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_1_lh_native.label 44 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_2_lh_native.label 45 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_3_lh_native.label 46 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_4_lh_native.label 47 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_5_lh_native.label 48 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_1_lh_native.label 49 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_2_lh_native.label 50 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_3_lh_native.label

7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --hemi lh sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 50 LabelThresh 0 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig 0 1336330 Net_10_ROIs_1_lh_native 1 1639705 Net_11_ROIs_1_lh_native 2 2647065 Net_12_ROIs_1_lh_native 3 11829830 Net_12_ROIs_2_lh_native 4 25700 Net_13_ROIs_1_lh_native 5 16399044 Net_13_ROIs_2_lh_native 6 6500 Net_13_ROIs_3_lh_native 7 3294840 Net_13_ROIs_4_lh_native 8 660700 Net_13_ROIs_5_lh_native 9 6558940 Net_14_ROIs_1_lh_native 10 7874740 Net_14_ROIs_2_lh_native 11 14465658 Net_14_ROIs_3_lh_native 12 9180300 Net_14_ROIs_4_lh_native 13 12300 Net_14_ROIs_5_lh_native 14 9182740 Net_15_ROIs_1_lh_native 15 3296035 Net_16_ROIs_1_lh_native 16 9211105 Net_16_ROIs_2_lh_native 17 4924360 Net_17_ROIs_1_lh_native 18 3302560 Net_17_ROIs_2_lh_native 19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native 21 13777468 Net_18_ROIs_1_lh_native 22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native 24 3294765 Net_18_ROIs_4_lh_native 25 14443610 Net_18_ROIs_5_lh_native 26 10511400 Net_19_ROIs_1_lh_native 27 8323072 Net_2_ROIs_1_lh_native 28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native 30 1316060 Net_3_ROIs_2_lh_native 31 14464220 Net_3_ROIs_3_lh_native 32 8323072 Net_4_ROIs_1_lh_native 33 7874740 Net_5_ROIs_1_lh_native 34 9180300 Net_5_ROIs_2_lh_native 35 8860211 Net_5_ROIs_3_lh_native 36 9182740 Net_5_ROIs_4_lh_native 37 3296035 Net_6_ROIs_1_lh_native 38 9211105 Net_6_ROIs_2_lh_native 39 4924360 Net_6_ROIs_3_lh_native 40 3302560 Net_7_ROIs_1_lh_native 41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native 45 3302620 Net_8_ROIs_4_lh_native 46 10811612 Net_8_ROIs_5_lh_native 47 2637020 Net_9_ROIs_1_lh_native 48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot

Thanks,

Ben

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On Tue, Jun 14, 2022 at 1:33 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,

I was able to reproduce the core dump. In my case, it was because a mismatch of color scheme between input annotation file and the color table loaded with the surface.

I suspect it might be the same issue for you too. But I’m not sure what the right action is to work around this.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Friday, June 10, 2022 11:47 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi there,

Having issues with the following command:

mri_label2vol --annot lh.yeo_2011.annot --temp /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz --hemi lh --fill-ribbon --identity --subject sub-DAEK --o lh.sub-DAEK_annot_nat.nii.gz

produces the following error:

Number of labels: 0 Annot File: lh.yeo_2011.annot Template Volume: /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz Outut Volume: lh.sub-DAEK_annot_nat.nii.gz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: sub-DAEK Hemi: lh UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects 7.2.0 Template RAS-to-Vox: -------- -1.25000 -0.00000 -0.00000 160.00000; -0.00000 -0.00000 -1.25000 160.00000; -0.00000 1.25000 -0.00000 160.00000; -0.00000 -0.00000 -0.00000 1.00000; Template Voxel Volume: 0.512 nHits Thresh: 0 Using Identity Matrix RegMat: -------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Label RAS-to-Vox: -------- -1.25000 0.00000 0.00000 160.00000; 0.00000 0.00000 -1.25000 160.00000; 0.00000 1.25000 0.00000 160.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.white nvertices = 253237 Reading thickness /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.thickness Loading annotations from lh.yeo_2011.annot annotidmax = 48 nlabels = 48 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgz Mapping Segmentation fault

But when I run the same command without fill-ribbon the process runs to completion.

Not sure if this is a memory issue or something else.

Ben

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University

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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1FUT55eeYf35M-JkMc7UcSX6tQwoolQhFqBp-8LICAUTK0wswJKgW_N0VLBuD8TraBJXxv3A6xEtjOi3zHO6u6hS8qtjCvZLT8blEvNFm05eSJH6b8e3aKqHBqbtFAVOULtn9jgTodt8mPW8m3GmSRUmYpxpu9C3Fkzsso7QpJnn8ogCvZ1glcbo1qzY7f0tbdno7w-kyEgSnfbCNbMMoMyfrKVBy_uY9PmTLYP1fcwc9XbQsn81kFW3GvhlFpwBGRN3Le_la1zqvtr5WRJXwA7glAv3TYsHu2WOT_uygJjXNbYUcMNoxCuIb_tjOc9SD/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/129Kw4R0yoVeTC6bBd1uPUqKUYuQfV-mbD5MR0g-xyo9r99gu2Z-4tY7718A6CVUVsK1u7S1awCDro02sozDsoDFvIHYrhSD5vMlHw_EqisjHZyR11ZdEG2yXwgzu8-sfddrPtz3WvbkujxTvALD-PjFOcUYI_NvZuv-09oniwNIjtKWtpQ32jhSYbp70bpRYQbXH0r71ZqTKS8pYf708p8tjI23a7uEnlutWE573EHFSyZ96N8DYzjiawb99BHqVBLAHIt9CDL5wOEykkXYkYd_eyC6CASQ3k0otyq32qfMyZs0UoWTGjs1OtVTWvtUe/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/129Kw4R0yoVeTC6bBd1uPUqKUYuQfV-mbD5MR0g-xyo9r99gu2Z-4tY7718A6CVUVsK1u7S1awCDro02sozDsoDFvIHYrhSD5vMlHw_EqisjHZyR11ZdEG2yXwgzu8-sfddrPtz3WvbkujxTvALD-PjFOcUYI_NvZuv-09oniwNIjtKWtpQ32jhSYbp70bpRYQbXH0r71ZqTKS8pYf708p8tjI23a7uEnlutWE573EHFSyZ96N8DYzjiawb99BHqVBLAHIt9CDL5wOEykkXYkYd_eyC6CASQ3k0otyq32qfMyZs0UoWTGjs1OtVTWvtUe/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1KFYgeucywv-sgvlszrUVmMExT1D1wTosDU5A-ke32OnzTiJE16BPNnIWUUrRFHCfQlcwzvjB9Q_K1vkrSEJCUQDTLqRHU2UEQjr1vhUytcvG7hKX9glUJjoxbSUY8O_1bQYvpZ7TOKLJ9YXI87fsdsCjOCH8pB3fiIxiezlWu0z6nZe6wVVSJFDrDdBem0x4EW9r5DDygdavp_pb5Y0W7eDFR-iX1WCGnPMNjDjpXexXTIdI_Ol2eLqKWFGHW4MUrUqdaqwYDldwTkGvUFz36lUI7bBBSR8z1QvvqnzPopmvsUdYFcp1-fYYTK9hnrhV/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1KBqYHmYqf-cm-adopQpa1hFDYwc2XxJdOhqXuwG4-p6H_zGJt9CzUb5Bcvty-89vJmkrh4_Y832uL8-DrSaORXDjxvEkwEs8RtxEuQq6lUEUmTfDzlsSL76rkunUEu1FsCKZ4XZ2Wo3E5uXvAb9ZbgagP66-F2BJ-VUqW_2K-K6ArkhyxeOBbFK_7nQsQrvVhi-lxaWl99ahxDwxvyDw0a4G2bKYecYvPx4JDXZOIqOnUJXhrMxb6r-ORsKccILBkvac-C0TUvVDohtWjtbk5SAJgnuIecC_IkYNBNjmdIGPIAtOk50-zSkafZunnfTb/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1KBqYHmYqf-cm-adopQpa1hFDYwc2XxJdOhqXuwG4-p6H_zGJt9CzUb5Bcvty-89vJmkrh4_Y832uL8-DrSaORXDjxvEkwEs8RtxEuQq6lUEUmTfDzlsSL76rkunUEu1FsCKZ4XZ2Wo3E5uXvAb9ZbgagP66-F2BJ-VUqW_2K-K6ArkhyxeOBbFK_7nQsQrvVhi-lxaWl99ahxDwxvyDw0a4G2bKYecYvPx4JDXZOIqOnUJXhrMxb6r-ORsKccILBkvac-C0TUvVDohtWjtbk5SAJgnuIecC_IkYNBNjmdIGPIAtOk50-zSkafZunnfTb/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1pg-D_wLryyZksJTKvQ2XCj2jB5SkB2H8DVHgj5FtQzPyNkniuHdTaL_IBFsxabyNQVwyDAGRDb0cGEIzTIwtcuvIjwV3Lg7QiLDyCU74wL7e7OWYfCCCREmXi9pTrSNypqR7dIGxdS9SqZWfBT2kNZZz3MP8T3iMaDPJB9tUGA0ftI51Y1MpTzJb0BuB7LpTw9riLUlNPvZd3ibg1m7sC629TtuUgdOT-UbH-LxXKgxPhoGJTq0JLzVzIVxqiHbwMlHBsuO84niKNg6mU818Tct_f3UyRX5FTrDYdFHzIsp8PP-5erbf9ISg_MOJtcBAuHtG9F7ocoXiqQITXSSQuw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1ewws5jb1hRDkswPgWMqJP5exouHEKg_qKAlpTyoWlL_21LVGF-OMt6D7Slbg57sQbZwXOVLoDnC9YmdlJJzCPz_HQflF5OSUSoOzRFqBb6S3Zj7jBeo3gp2dpeZTH5IAbvwMwJpAhQONN1708QcTAGvm0HQozK-hXCPgp3gdbe5lVhSGPdR8e1sEZJXq-rZdgdTLIf1a_-e1YvYd5r2ev1HhSuWmyQ5RsQA7Bcb_Rh2TEkdyOmIr0twh52ig6Lrx-_i0r-cciGHcHqmJL_nfrTjOePOVj-htPLFiL1A6BFbEZOUR5-kiUNSZMT9PrStO3fWQUbb7X1WIRA8SBCJQXg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1ewws5jb1hRDkswPgWMqJP5exouHEKg_qKAlpTyoWlL_21LVGF-OMt6D7Slbg57sQbZwXOVLoDnC9YmdlJJzCPz_HQflF5OSUSoOzRFqBb6S3Zj7jBeo3gp2dpeZTH5IAbvwMwJpAhQONN1708QcTAGvm0HQozK-hXCPgp3gdbe5lVhSGPdR8e1sEZJXq-rZdgdTLIf1a_-e1YvYd5r2ev1HhSuWmyQ5RsQA7Bcb_Rh2TEkdyOmIr0twh52ig6Lrx-_i0r-cciGHcHqmJL_nfrTjOePOVj-htPLFiL1A6BFbEZOUR5-kiUNSZMT9PrStO3fWQUbb7X1WIRA8SBCJQXg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1ohxFwDlj95GLWi92_zXWezKzkZSexk4R2BjNZnepB4disZNNuSpW1kK96h-7gzHWzHAfWDFB-dq5WFtrzogG_IDQxfKJM9_8THWm2gTlYr7E4JMzy50EQ0biIxFBc18A7TnYbRKYCW423M2Et_XUa845uEAbuqGRY-rPn8VINSo8n-KcLzZVfZIDWMcJfZiUh7nY6YlsjtlsatA_dXwilbQbksrtIoKDz9rGY5xmZZBLw_VbP8y8YHRyqOrPg4z8ic10lMUnmQgTlmAQ2YgWJ1xKBUPxs5Yk4ek3dLoLkM-g8rkKGlnK7y8aIl9YsPhk/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1gWC8FomBEWvS9SwG5Wk_5Npjvbjt5_29f_qSVE6r4gTYuQr1OZ3heuVWDhm6ygbJNNjl1rcmbLynrODhMW7zGVFOVKJuo9VGT_6ZzY4tD4lpW48h_e3rKiASiRE6iSmhswYQZU3h8c7vDBMokS0is2ROd2vxRcBpVk8R4coPUJm4HAxL7IJkyp9T1IOseEkAQ6Evmgof8igvqcLT9jVdvH6LXAARWQN8TW7ZoIwVtabTajMFOgP-2A0Kg_EmGcDvJqIrVwP2p0e0olstkbXWUkMW1IkROWarolKJ4h73QIjEXEmYKXqsMD_PaNG0quCB/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1gWC8FomBEWvS9SwG5Wk_5Npjvbjt5_29f_qSVE6r4gTYuQr1OZ3heuVWDhm6ygbJNNjl1rcmbLynrODhMW7zGVFOVKJuo9VGT_6ZzY4tD4lpW48h_e3rKiASiRE6iSmhswYQZU3h8c7vDBMokS0is2ROd2vxRcBpVk8R4coPUJm4HAxL7IJkyp9T1IOseEkAQ6Evmgof8igvqcLT9jVdvH6LXAARWQN8TW7ZoIwVtabTajMFOgP-2A0Kg_EmGcDvJqIrVwP2p0e0olstkbXWUkMW1IkROWarolKJ4h73QIjEXEmYKXqsMD_PaNG0quCB/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1-Co0Tj3nO9PKVc4FF5EYp-pbwW1MSBhpVRo4lPgCIr_Le-jinRghImfaUz1XwH3bS9-3JJtGF7iqyCINnenimFyLBFGtPvkx4gKT4LM_XuqtA8yehAilreaW-7tfG7rFm9CKmyvL6UTMUL8ixh3tIeZDVlTa-WL09UQo8OB3xQPLEOyeBBTdvYOD9-EejJcMmPhvCbVyM7VATQc4WnF3BT3C9Wr5Fp2UY25cbOG0IiS9S3TID8jUqddMj_O_8SHKh8odIuW_MNbPu35lVuaMTi9Gh9V0u7p3tOIkH4vOTMN-8GTlTCP5safglQWXvSSt/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1nUKsaivbAuxJojvr0yFs7hY0LXQON0_HrlCUPtW5ymN-QLI0xMSE64vbmxo74tTH5VaFyluU46uvw3l-Oi9Zs6J_C9ApmKC6YBCM7Vp9dxkgV2G-JQiYfsxps_neYqUYs3Ex6cqTkpvxd29lBZXFfOAAEuEh89KJ9t3RbBTeOlzXr_mxGPrA9_wXx5Ik_NMVLgPT_qhUj3n03BUZBWoYAS8fR1HG-dDJAvMSNEIbB4DEEaIO1w4toFS_NkYAtb0_kF5ch2aEyPtKeAXZXAQNHORaUhvK4OmoxzwZuVrxEFBj3kjicTmAplnxy8Ns7pjx/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1nUKsaivbAuxJojvr0yFs7hY0LXQON0_HrlCUPtW5ymN-QLI0xMSE64vbmxo74tTH5VaFyluU46uvw3l-Oi9Zs6J_C9ApmKC6YBCM7Vp9dxkgV2G-JQiYfsxps_neYqUYs3Ex6cqTkpvxd29lBZXFfOAAEuEh89KJ9t3RbBTeOlzXr_mxGPrA9_wXx5Ik_NMVLgPT_qhUj3n03BUZBWoYAS8fR1HG-dDJAvMSNEIbB4DEEaIO1w4toFS_NkYAtb0_kF5ch2aEyPtKeAXZXAQNHORaUhvK4OmoxzwZuVrxEFBj3kjicTmAplnxy8Ns7pjx/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1vY_16Zjww2xu0uzWyiUohSSGGRD2H3nPfBx-WboNIK-KoK15rtSqkX2N-vmZ_cZ27ff2CpMOXLf512LEyZ_evkkY3h5Fj3fd8kZmWMbNzbz13qEX-J_IC_P6asO8e2VQ_smAoIOlIkFkOJHjdqGr04XT2bVWuPZjC9dOlUH26F47LauKhAEPdxCKLr4NE9Pv3ivq0eZZ5kFH0bqLzGyz0nNRpBvXgkwvnlq8hqiHZ8Bxe0h2o9TE0GEYSMPGRmj3BKHyBYVGLsX58dmumT-cSW8AEvkCb91oK2Lv-DywOJBySAA4UnwaUtsPVsa-Qaz80DhUEKpRssMKaD0KwpO1-Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1KyPIPmRNwus-z79lEGn0T7diD2lNJqoI2KIQh4lMv2faOIlvJOXCKLsN35WtRkxw61rareTh_XeaqS274mShL_BwFF0zrupuNsCOKEU94cyu7wYoAM6A93LTuYfY69rB1_3laFePNZaecZtHzcaAqoooOI2HEKJu89TZc6ronKly_Y7oIPveyaULOt3u4wFYCT2PowbhyLRJ5rEfGIkGksjlIxIB46ynWAQuDbi1KJPj7YPc039Tros_bYxNL_UjuGzrk_VVjobmcicqBvJbHh69MPWijPmHDSLTSx76IPcDo85-lkMmm_-3yhZXEoMMFwMXN-kGs8rg9zY0wYgyNQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1KyPIPmRNwus-z79lEGn0T7diD2lNJqoI2KIQh4lMv2faOIlvJOXCKLsN35WtRkxw61rareTh_XeaqS274mShL_BwFF0zrupuNsCOKEU94cyu7wYoAM6A93LTuYfY69rB1_3laFePNZaecZtHzcaAqoooOI2HEKJu89TZc6ronKly_Y7oIPveyaULOt3u4wFYCT2PowbhyLRJ5rEfGIkGksjlIxIB46ynWAQuDbi1KJPj7YPc039Tros_bYxNL_UjuGzrk_VVjobmcicqBvJbHh69MPWijPmHDSLTSx76IPcDo85-lkMmm_-3yhZXEoMMFwMXN-kGs8rg9zY0wYgyNQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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‘35 11223921 cluster35’ is randomly generated color scheme from mris_label2annot.

Not sure how you ran mri_annotation2label. But it looks like you are missing label file for corpuscallosum. The output should be correct if you fix that.

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Benjamin Deck Sent: Monday, June 27, 2022 10:42 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

Sorry. I broke apart the annotation file to get the labels using mri_annotation2label. Then simply tried to reconstruct it.

Ben

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On Mon, Jun 27, 2022 at 10:31 AM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,

Sorry for all the troubles.

I’m trying to reproduce here. I found aparc.annot.ctab in bert directory. I have a question about the label files. Are they part of the tutorial data? Where did you download the data? I don’t see those label files in the directory.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Sunday, June 26, 2022 3:02 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution So I thought that since this has caused me many issues I would test this on the bert subject using aparc.annot. These are default with freesurfer.

command using Bert: cwd /mnt/c/Users/Ben/freesurfer/subjects/bert/label cmdline mris_label2annot --s bert --hemi lh --ctab /mnt/c/Users/Ben/freesurfer/subjects/bert/label/aparc.annot.ctab --a myaparc --ldir /mnt/c/Users/Ben/freesurfer/subjects/bert/label/ sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject bert hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable /mnt/c/Users/Ben/freesurfer/subjects/bert/label/aparc.annot.ctab AnnotName myaparc nlables 35 LabelThresh 0 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/bert/surf/lh.orig 1 2647065 bankssts 2 10511485 caudalanteriorcingulate 3 6500 caudalmiddlefrontal 4 6558940 cuneus 5 660700 entorhinal 6 9231540 fusiform 7 14433500 inferiorparietal 8 7874740 inferiortemporal 9 9180300 isthmuscingulate 10 9182740 lateraloccipital 11 3296035 lateralorbitofrontal 12 9211105 lingual 13 4924360 medialorbitofrontal 14 3302560 middletemporal 15 3988500 parahippocampal 16 3988540 paracentral 17 9221340 parsopercularis 18 3302420 parsorbitalis 19 1326300 parstriangularis 20 3957880 pericalcarine 21 1316060 postcentral 22 14464220 posteriorcingulate 23 14423100 precentral 24 11832480 precuneus 25 9180240 rostralanteriorcingulate 26 8204875 rostralmiddlefrontal 27 10542100 superiorfrontal 28 9221140 superiorparietal 29 14474380 superiortemporal 30 1351760 supramarginal 31 6553700 frontalpole 32 11146310 temporalpole 33 13145750 transversetemporal 34 2146559 insula 35 11223921 cluster35 Mapping unhit to unknown Found 0 unhit vertices Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/bert/label/lh.myaparc.annot _____________________________________________________________________

It seems to be not indexing properly into the CTAB file

CTAB:

0 unknown 25 5 25 0 1 bankssts 25 100 40 0 2 caudalanteriorcingulate 125 100 160 0 3 caudalmiddlefrontal 100 25 0 0 4 corpuscallosum 120 70 50 0 5 cuneus 220 20 100 0 6 entorhinal 220 20 10 0 7 fusiform 180 220 140 0 8 inferiorparietal 220 60 220 0 9 inferiortemporal 180 40 120 0 10 isthmuscingulate 140 20 140 0 11 lateraloccipital 20 30 140 0 12 lateralorbitofrontal 35 75 50 0 13 lingual 225 140 140 0 14 medialorbitofrontal 200 35 75 0 15 middletemporal 160 100 50 0 16 parahippocampal 20 220 60 0 17 paracentral 60 220 60 0 18 parsopercularis 220 180 140 0 19 parsorbitalis 20 100 50 0 20 parstriangularis 220 60 20 0 21 pericalcarine 120 100 60 0 22 postcentral 220 20 20 0 23 posteriorcingulate 220 180 220 0 24 precentral 60 20 220 0 25 precuneus 160 140 180 0 26 rostralanteriorcingulate 80 20 140 0 27 rostralmiddlefrontal 75 50 125 0 28 superiorfrontal 20 220 160 0 29 superiorparietal 20 180 140 0 30 superiortemporal 140 220 220 0 31 supramarginal 80 160 20 0 32 frontalpole 100 0 100 0 33 temporalpole 70 20 170 0 34 transversetemporal 150 150 200 0 35 insula 255 192 32 0

I really have no idea why it returns this nondescript cluster 35--- there shouldn't be a cluster 35.

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On Fri, Jun 24, 2022 at 5:10 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: I noticed two things: 1. you have skipped numbers in label files output - make sure all label names in LUT have corresponding label files hemi.label-name.label in ldir directory. 2. your annotation output doesn’t agree with the LUT your showed - make sure you are passing the correct copy to mris_label2annot

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Friday, June 24, 2022 4:47 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

I just re-ran this and I am now noticing something else that is strange.

I included an "unknown 0 0 0 0" row at the beginning and gave this a 0 index. Similar to the default LUT

LUT: 0 Unknown 255 255 255 0 1 Net_14_ROIs_4_native 25 5 25 0 2 Net_9_ROIs_1_native 25 100 40 0 3 Net_18_ROIs_4_native 70 130 180 0

My command and output:

mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --ctab sub-DAEK_yeoLUT.txt --maxstatwinner --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019/ Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 57 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 1 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_14_ROIs_4_native.label 2 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_9_ROIs_1_native.label 3 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_18_ROIs_4_native.label 4 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_8_ROIs_1_native.label 5 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_14_ROIs_1_native.label 7 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_14_ROIs_2_native.label 8 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_6_ROIs_1_native.label 10 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_9_ROIs_2_native.label 11 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_8_ROIs_3_native.label 12 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_17_ROIs_3_native.label 13 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_10_ROIs_1_native.label 14 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_5_ROIs_3_native.label 15 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_16_ROIs_2_native.label 16 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_5_ROIs_4_native.label 17 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_9_ROIs_3_native.label 18 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_18_ROIs_3_native.label 20 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_13_ROIs_2_native.label 21 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_2_ROIs_1_native.label 23 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_5_ROIs_1_native.label 24 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_13_ROIs_1_native.label 25 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_8_ROIs_4_native.label 26 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_13_ROIs_3_native.label 27 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_8_ROIs_2_native.label 28 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_18_ROIs_5_native.label 29 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_17_ROIs_2_native.label 30 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_12_ROIs_1_native.label 31 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_3_ROIs_3_native.label 32 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_18_ROIs_1_native.label 33 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_11_ROIs_1_native.label 35 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_3_ROIs_2_native.label 36 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_6_ROIs_2_native.label 37 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_13_ROIs_4_native.label 39 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_15_ROIs_1_native.label 40 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_7_ROIs_1_native.label 41 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_18_ROIs_2_native.label 42 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_19_ROIs_1_native.label 43 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_2_ROIs_2_native.label 44 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_5_ROIs_2_native.label 45 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_16_ROIs_1_native.label 46 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_14_ROIs_5_native.label 47 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_13_ROIs_5_native.label 48 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_3_ROIs_1_native.label 49 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_7_ROIs_2_native.label 50 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_12_ROIs_2_native.label 51 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_8_ROIs_5_native.label 52 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_17_ROIs_4_native.label 53 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_4_ROIs_1_native.label 54 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_17_ROIs_1_native.label 55 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_14_ROIs_3_native.label 56 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019//lh.Net_6_ROIs_3_native.label

7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019 cmdline mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --ctab sub-DAEK_yeoLUT.txt --maxstatwinner --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019/ sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 50 LabelThresh 0 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig 1 2647065 Net_9_ROIs_1_native 2 11829830 Net_18_ROIs_4_native 3 25700 Net_8_ROIs_1_native 4 16399044 Net_14_ROIs_1_native 5 3294840 Net_14_ROIs_2_native 6 660700 Net_6_ROIs_1_native 7 7874740 Net_9_ROIs_2_native 8 14465658 Net_8_ROIs_3_native 9 9180300 Net_17_ROIs_3_native 10 12300 Net_10_ROIs_1_native 11 9182740 Net_5_ROIs_3_native 12 3296035 Net_16_ROIs_2_native 13 9211105 Net_5_ROIs_4_native 14 4924360 Net_9_ROIs_3_native 15 3302560 Net_18_ROIs_3_native 16 3988540 Net_13_ROIs_2_native 17 13777468 Net_2_ROIs_1_native 18 3302420 Net_5_ROIs_1_native 19 3294765 Net_13_ROIs_1_native 20 14443610 Net_8_ROIs_4_native 21 10511400 Net_13_ROIs_3_native 22 8323072 Net_8_ROIs_2_native 23 1326300 Net_18_ROIs_5_native 24 3957880 Net_17_ROIs_2_native 25 1316060 Net_12_ROIs_1_native 26 14464220 Net_3_ROIs_3_native 27 8323072 Net_18_ROIs_1_native 28 7874740 Net_11_ROIs_1_native 29 8860211 Net_3_ROIs_2_native 30 9182740 Net_6_ROIs_2_native 31 3296035 Net_13_ROIs_4_native 32 4924360 Net_15_ROIs_1_native 33 3302560 Net_7_ROIs_1_native 34 3988500 Net_18_ROIs_2_native 35 3988540 Net_19_ROIs_1_native 36 9221340 Net_2_ROIs_2_native 37 3302420 Net_5_ROIs_2_native 38 3302620 Net_16_ROIs_1_native 39 10811612 Net_14_ROIs_5_native 40 2637020 Net_13_ROIs_5_native 41 1326300 Net_3_ROIs_1_native 42 3957880 Net_7_ROIs_2_native 43 1316060 Net_12_ROIs_2_native 44 14464220 Net_8_ROIs_5_native 45 14423100 Net_17_ROIs_4_native 46 11832480 Net_4_ROIs_1_native 47 9180240 Net_17_ROIs_1_native 48 8204875 Net_14_ROIs_3_native 49 10542100 Net_6_ROIs_3_native 50 3840729 cluster50 Mapping unhit to unknown Found 19023 unhit vertices Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot

For some very weird reason it skips my 0 row, 'unknown' and then adds an undescript cluster at the end.

Why is that occurring?

Ben

On Fri, Jun 24, 2022 at 4:00 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,

Based on your command line options (‘—no-unknown –offset 0’) and output, I believe your LUT starts with ‘0 Net_10_ROIs_1_lh_native 255 255 255 0’ not ‘0 Unknown 0 0 0 0’. Can you double check the LUT you passed to mris_label2annot?

I was able to reproduce the crash with duplicated color scheme scenario. Once you fix duplicated color schemes in your LUT, ‘mris_label2vol –fill-ribbon’ should run fine.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Thursday, June 23, 2022 10:42 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hmm.. I see what you're saying not the names but the actual location. Shouldn't I be getting a warning of overlapping labels and therefore an arg like --maxstatwinner would be helpful?

On Thu, Jun 23, 2022 at 10:34 AM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: For the duplicates, 19 is same as 41, 20 is same as 42, …

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Thursday, June 23, 2022 10:27 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

Thanks for your continued support on this issue.

Addressing your first question.

If I use --offset 1 then the get the following:

cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --offset 1 sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 50 LabelThresh 1 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig 1 1639705 Net_11_ROIs_1_lh_native 2 2647065 Net_12_ROIs_1_lh_native 3 11829830 Net_12_ROIs_2_lh_native 4 25700 Net_13_ROIs_1_lh_native 5 16399044 Net_13_ROIs_2_lh_native 6 6500 Net_13_ROIs_3_lh_native 7 3294840 Net_13_ROIs_4_lh_native 8 660700 Net_13_ROIs_5_lh_native 9 6558940 Net_14_ROIs_1_lh_native 10 7874740 Net_14_ROIs_2_lh_native 11 14465658 Net_14_ROIs_3_lh_native 12 9180300 Net_14_ROIs_4_lh_native 13 12300 Net_14_ROIs_5_lh_native 14 9182740 Net_15_ROIs_1_lh_native 15 3296035 Net_16_ROIs_1_lh_native 16 9211105 Net_16_ROIs_2_lh_native 17 4924360 Net_17_ROIs_1_lh_native 18 3302560 Net_17_ROIs_2_lh_native 19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native 21 13777468 Net_18_ROIs_1_lh_native 22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native 24 3294765 Net_18_ROIs_4_lh_native 25 14443610 Net_18_ROIs_5_lh_native 26 10511400 Net_19_ROIs_1_lh_native 27 8323072 Net_2_ROIs_1_lh_native 28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native 30 1316060 Net_3_ROIs_2_lh_native 31 14464220 Net_3_ROIs_3_lh_native 32 8323072 Net_4_ROIs_1_lh_native 33 7874740 Net_5_ROIs_1_lh_native 34 9180300 Net_5_ROIs_2_lh_native 35 8860211 Net_5_ROIs_3_lh_native 36 9182740 Net_5_ROIs_4_lh_native 37 3296035 Net_6_ROIs_1_lh_native 38 9211105 Net_6_ROIs_2_lh_native 39 4924360 Net_6_ROIs_3_lh_native 40 3302560 Net_7_ROIs_1_lh_native 41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native 45 3302620 Net_8_ROIs_4_lh_native 46 10811612 Net_8_ROIs_5_lh_native 47 2637020 Net_9_ROIs_1_lh_native 48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native 50 791413 cluster50 Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot

Where cluster50 is some nondescript cluster and it ignores my network 10 which should be the first entry.

To address your second question about duplicates.

19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native

While these may look almost like duplicates they are different rois within the same larger network. This separation is important for what I am doing so I need to keep the ROIs separate from one another but they are a part of the same larger network. However, Freesurfer doesn't know that they are.

On Thu, Jun 23, 2022 at 10:17 AM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: I am confused about ‘—no-unknown –offset 0’. Your output doesn’t seem agree with the codes. If your label starts at 1, I think it should be ‘—offset 1’ instead of 0. Can you double check your LUT?

I see duplicates in second column of these lines: (second column is calculated from RGB values.)

19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native

22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native

28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native

41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native

48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Thursday, June 23, 2022 9:36 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

I am not seeing any duplicates--highlighting wasn't rendered on my end.

my LUT:

0 Unknown 0 0 0 0 1 Net_10_ROIs_1_lh_native 255 255 255 0 2 Net_11_ROIs_1_lh_native 25 5 25 0 3 Net_12_ROIs_1_lh_native 25 100 40 0 4 Net_12_ROIs_2_lh_native 70 130 180 0 5 Net_13_ROIs_1_lh_native 100 100 0 0 6 Net_13_ROIs_2_lh_native 196 58 250 0

which is why I gave the --offset flag as 0 for --no-unknown

I did notice that the labels is incorrect. So for some reason, it seems to be missing two labels that exist in the annotation. That is strange.

Ben

On Thu, Jun 23, 2022 at 8:55 AM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: How does your LUT look like? What is your first line?

For left hemi, your loaded 50 label files to mris_label2annot, but mri_label2vol only reported 48 labels. It looks like you have duplicated RGB in your LUT. I have identified some. See highlighted in red. The duplicated RGB entries can cause problems.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Wednesday, June 22, 2022 2:24 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

Sure thing.

Commands:

mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt

Output: Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 105 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 1 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_10_ROIs_1_lh_native.label 2 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_11_ROIs_1_lh_native.label 3 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_1_lh_native.label 4 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_2_lh_native.label 5 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_1_lh_native.label 6 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_2_lh_native.label 7 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_3_lh_native.label 8 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_4_lh_native.label 9 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_5_lh_native.label 10 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_1_lh_native.label 11 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_2_lh_native.label 12 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_3_lh_native.label 13 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_4_lh_native.label 14 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_5_lh_native.label 15 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_15_ROIs_1_lh_native.label 16 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_1_lh_native.label 17 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_2_lh_native.label 18 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_1_lh_native.label 19 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_2_lh_native.label 20 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_3_lh_native.label 21 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_4_lh_native.label 22 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_1_lh_native.label 23 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_2_lh_native.label 24 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_3_lh_native.label 25 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_4_lh_native.label 26 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_5_lh_native.label 27 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_19_ROIs_1_lh_native.label 28 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_1_lh_native.label 29 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_2_lh_native.label 30 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_1_lh_native.label 31 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_2_lh_native.label 32 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_3_lh_native.label 33 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_4_ROIs_1_lh_native.label 34 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_1_lh_native.label 35 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_2_lh_native.label 36 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_3_lh_native.label 37 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_4_lh_native.label 38 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_1_lh_native.label 39 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_2_lh_native.label 40 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_3_lh_native.label 41 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_1_lh_native.label 42 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_2_lh_native.label 43 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_1_lh_native.label 44 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_2_lh_native.label 45 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_3_lh_native.label 46 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_4_lh_native.label 47 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_5_lh_native.label 48 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_1_lh_native.label 49 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_2_lh_native.label 50 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_3_lh_native.label

7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --hemi lh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 50 LabelThresh 1 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig 0 16777215 Net_10_ROIs_1_lh_native 1 1639705 Net_11_ROIs_1_lh_native 2 2647065 Net_12_ROIs_1_lh_native 3 11829830 Net_12_ROIs_2_lh_native 4 25700 Net_13_ROIs_1_lh_native 5 16399044 Net_13_ROIs_2_lh_native 6 6500 Net_13_ROIs_3_lh_native 7 3294840 Net_13_ROIs_4_lh_native 8 660700 Net_13_ROIs_5_lh_native 9 6558940 Net_14_ROIs_1_lh_native 10 7874740 Net_14_ROIs_2_lh_native 11 14465658 Net_14_ROIs_3_lh_native 12 9180300 Net_14_ROIs_4_lh_native 13 12300 Net_14_ROIs_5_lh_native 14 9182740 Net_15_ROIs_1_lh_native 15 3296035 Net_16_ROIs_1_lh_native 16 9211105 Net_16_ROIs_2_lh_native 17 4924360 Net_17_ROIs_1_lh_native 18 3302560 Net_17_ROIs_2_lh_native 19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native 21 13777468 Net_18_ROIs_1_lh_native 22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native 24 3294765 Net_18_ROIs_4_lh_native 25 14443610 Net_18_ROIs_5_lh_native 26 10511400 Net_19_ROIs_1_lh_native 27 8323072 Net_2_ROIs_1_lh_native 28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native 30 1316060 Net_3_ROIs_2_lh_native 31 14464220 Net_3_ROIs_3_lh_native 32 8323072 Net_4_ROIs_1_lh_native 33 7874740 Net_5_ROIs_1_lh_native 34 9180300 Net_5_ROIs_2_lh_native 35 8860211 Net_5_ROIs_3_lh_native 36 9182740 Net_5_ROIs_4_lh_native 37 3296035 Net_6_ROIs_1_lh_native 38 9211105 Net_6_ROIs_2_lh_native 39 4924360 Net_6_ROIs_3_lh_native 40 3302560 Net_7_ROIs_1_lh_native 41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native 45 3302620 Net_8_ROIs_4_lh_native 46 10811612 Net_8_ROIs_5_lh_native 47 2637020 Net_9_ROIs_1_lh_native 48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot

command: mris_label2annot --s sub-DAEK --hemi rh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt

output: Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 105 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 51 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_10_ROIs_1_rh_native.label 52 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_11_ROIs_1_rh_native.label 53 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_12_ROIs_1_rh_native.label 54 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_12_ROIs_2_rh_native.label 55 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_1_rh_native.label 56 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_2_rh_native.label 57 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_3_rh_native.label 58 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_4_rh_native.label 59 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_1_rh_native.label 60 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_2_rh_native.label 61 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_3_rh_native.label 62 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_4_rh_native.label 63 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_5_rh_native.label 64 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_15_ROIs_1_rh_native.label 65 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_1_rh_native.label 66 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_2_rh_native.label 67 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_3_rh_native.label 68 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_1_rh_native.label 69 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_2_rh_native.label 70 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_3_rh_native.label 71 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_4_rh_native.label 72 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_1_rh_native.label 73 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_2_rh_native.label 74 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_3_rh_native.label 75 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_4_rh_native.label 76 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_19_ROIs_1_rh_native.label 77 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_2_ROIs_1_rh_native.label 78 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_2_ROIs_2_rh_native.label 79 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_1_rh_native.label 80 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_2_rh_native.label 81 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_3_rh_native.label 82 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_4_ROIs_1_rh_native.label 83 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_1_rh_native.label 84 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_2_rh_native.label 85 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_3_rh_native.label 86 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_4_rh_native.label 87 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_1_rh_native.label 88 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_2_rh_native.label 89 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_3_rh_native.label 90 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_1_rh_native.label 91 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_2_rh_native.label 92 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_3_rh_native.label 93 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_1_rh_native.label 94 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_2_rh_native.label 95 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_3_rh_native.label 96 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_4_rh_native.label 97 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_5_rh_native.label 98 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_6_rh_native.label 99 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_1_rh_native.label 100 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_2_rh_native.label 101 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_3_rh_native.label 102 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_4_rh_native.label 103 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_5_rh_native.label 104 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_6_rh_native.label

7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --hemi rh --a yeo2011 --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --no-unknown --offset 0 --ctab sub-DAEK_yeoLUT.txt sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi rh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 54 LabelThresh 1 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/rh.orig 0 1316060 Net_10_ROIs_1_rh_native 1 14464220 Net_11_ROIs_1_rh_native 2 14423100 Net_12_ROIs_1_rh_native 3 11832480 Net_12_ROIs_2_rh_native 4 9180240 Net_13_ROIs_1_rh_native 5 8204875 Net_13_ROIs_2_rh_native 6 10542100 Net_13_ROIs_3_rh_native 7 9231380 Net_13_ROIs_4_rh_native 8 9221140 Net_14_ROIs_1_rh_native 9 14474380 Net_14_ROIs_2_rh_native 10 2763429 Net_14_ROIs_3_rh_native 11 1351760 Net_14_ROIs_4_rh_native 12 15736992 Net_14_ROIs_5_rh_native 13 6553700 Net_15_ROIs_1_rh_native 14 11146310 Net_16_ROIs_1_rh_native 15 13145750 Net_16_ROIs_2_rh_native 16 3311482 Net_16_ROIs_3_rh_native 17 2146304 Net_17_ROIs_1_rh_native 18 5935475 Net_17_ROIs_2_rh_native 19 681085 Net_17_ROIs_3_rh_native 20 23060 Net_17_ROIs_4_rh_native 21 3957760 Net_18_ROIs_1_rh_native 22 3311482 Net_18_ROIs_2_rh_native 23 1321040 Net_18_ROIs_3_rh_native 24 3276922 Net_18_ROIs_4_rh_native 25 6588260 Net_19_ROIs_1_rh_native 26 3957760 Net_2_ROIs_1_rh_native 27 50372 Net_2_ROIs_2_rh_native 28 2671812 Net_3_ROIs_1_rh_native 29 3957956 Net_3_ROIs_2_rh_native 30 6564036 Net_3_ROIs_3_rh_native 31 3945156 Net_4_ROIs_1_rh_native 32 13127690 Net_5_ROIs_1_rh_native 33 6604880 Net_5_ROIs_2_rh_native 34 2647140 Net_5_ROIs_3_rh_native 35 3937480 Net_5_ROIs_4_rh_native 36 665610 Net_6_ROIs_1_rh_native 37 50372 Net_6_ROIs_2_rh_native 38 706590 Net_6_ROIs_3_rh_native 39 5923840 Net_7_ROIs_1_rh_native 40 6579200 Net_7_ROIs_2_rh_native 41 32768 Net_7_ROIs_3_rh_native 42 25600 Net_8_ROIs_1_rh_native 43 13117500 Net_8_ROIs_2_rh_native 44 6574090 Net_8_ROIs_3_rh_native 45 51200 Net_8_ROIs_4_rh_native 46 8320 Net_8_ROIs_5_rh_native 47 25750 Net_8_ROIs_6_rh_native 48 1336330 Net_9_ROIs_1_rh_native 49 25740 Net_9_ROIs_2_rh_native 50 3983360 Net_9_ROIs_3_rh_native 51 7895160 Net_9_ROIs_4_rh_native 52 6553720 Net_9_ROIs_5_rh_native 53 8312 Net_9_ROIs_6_rh_native Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/rh.yeo2011.annot

---Annotations look fine.

Command: mri_label2vol --o lh.yeo2011_in_nat.mgz --annot ../lh.yeo2011.annot --identity --fill-ribbon --subject sub-DAEK --h emi lh

Output: Number of labels: 0 Annot File: ../lh.yeo2011.annot Template Volume: (null) Outut Volume: lh.yeo2011_in_nat.mgz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: sub-DAEK Hemi: lh UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects 7.2.0 INFO: loading surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.white nvertices = 253237 Reading thickness /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.thickness Loading annotations from ../lh.yeo2011.annot annotidmax = 48 nlabels = 48 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgz Mapping Segmentation fault

----Same thing occurs for the right hemi

On Wed, Jun 22, 2022 at 11:42 AM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,

Do you mean the issue that ‘mri_label2vol –fill-ribbon’ crashes? Can you re-run and provide your mris_label2annot and mri_label2vol command line and output?

I’m not sure I will be able to offer work around, but I would like to understand the problem better for future development.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Tuesday, June 21, 2022 5:04 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

It seems that this did not solve the issue. Are there any other reasons why this would occur?

Ben

On Fri, Jun 17, 2022 at 2:59 PM Benjamin Deck <bdeck8317@gmail.commailto:bdeck8317@gmail.com> wrote: Hi Yujing,

Thank you. I will give it a try! Can documentation be updated?

Ben

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On Fri, Jun 17, 2022 at 2:56 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,

Just wanted to update you on mris_label2annot command line options.

If ‘--no-unknown’ is used with mris_label2annot, ‘—offset 1’ should also be specified.

Yujing

From: Huang, Yujing Sent: Thursday, June 16, 2022 1:59 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: RE: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

Hi Ben,

I’m learning it myself too.

I played it a little more. I see the mismatch can happen if you skip a number in you LUT.

Also, if you have ‘0 Unknown 0 0 0 0’ in your LUT, I’m not sure you should use ‘--no-unknown’ for mris_label2annot. It will cause your annotation off by one.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Thursday, June 16, 2022 10:58 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing,

Thanks for taking a look. What do you mean by mismatch?

The LUT was used to make the annot file. What would generate this mismatch?

Here is the output from my mris_label2annot call:

mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --hemi lh Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 105 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 1 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_10_ROIs_1_lh_native.label 2 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_11_ROIs_1_lh_native.label 3 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_1_lh_native.label 4 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_2_lh_native.label 5 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_1_lh_native.label 6 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_2_lh_native.label 7 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_3_lh_native.label 8 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_4_lh_native.label 9 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_5_lh_native.label 10 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_1_lh_native.label 11 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_2_lh_native.label 12 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_3_lh_native.label 13 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_4_lh_native.label 14 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_5_lh_native.label 15 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_15_ROIs_1_lh_native.label 16 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_1_lh_native.label 17 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_2_lh_native.label 18 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_1_lh_native.label 19 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_2_lh_native.label 20 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_3_lh_native.label 21 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_4_lh_native.label 22 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_1_lh_native.label 23 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_2_lh_native.label 24 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_3_lh_native.label 25 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_4_lh_native.label 26 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_5_lh_native.label 27 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_19_ROIs_1_lh_native.label 28 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_1_lh_native.label 29 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_2_lh_native.label 30 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_1_lh_native.label 31 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_2_lh_native.label 32 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_3_lh_native.label 33 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_4_ROIs_1_lh_native.label 34 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_1_lh_native.label 35 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_2_lh_native.label 36 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_3_lh_native.label 37 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_4_lh_native.label 38 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_1_lh_native.label 39 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_2_lh_native.label 40 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_3_lh_native.label 41 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_1_lh_native.label 42 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_2_lh_native.label 43 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_1_lh_native.label 44 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_2_lh_native.label 45 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_3_lh_native.label 46 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_4_lh_native.label 47 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_5_lh_native.label 48 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_1_lh_native.label 49 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_2_lh_native.label 50 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_3_lh_native.label

7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --hemi lh sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317

subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 50 LabelThresh 0 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig 0 1336330 Net_10_ROIs_1_lh_native 1 1639705 Net_11_ROIs_1_lh_native 2 2647065 Net_12_ROIs_1_lh_native 3 11829830 Net_12_ROIs_2_lh_native 4 25700 Net_13_ROIs_1_lh_native 5 16399044 Net_13_ROIs_2_lh_native 6 6500 Net_13_ROIs_3_lh_native 7 3294840 Net_13_ROIs_4_lh_native 8 660700 Net_13_ROIs_5_lh_native 9 6558940 Net_14_ROIs_1_lh_native 10 7874740 Net_14_ROIs_2_lh_native 11 14465658 Net_14_ROIs_3_lh_native 12 9180300 Net_14_ROIs_4_lh_native 13 12300 Net_14_ROIs_5_lh_native 14 9182740 Net_15_ROIs_1_lh_native 15 3296035 Net_16_ROIs_1_lh_native 16 9211105 Net_16_ROIs_2_lh_native 17 4924360 Net_17_ROIs_1_lh_native 18 3302560 Net_17_ROIs_2_lh_native 19 3988500 Net_17_ROIs_3_lh_native 20 3988540 Net_17_ROIs_4_lh_native 21 13777468 Net_18_ROIs_1_lh_native 22 9221340 Net_18_ROIs_2_lh_native 23 3302420 Net_18_ROIs_3_lh_native 24 3294765 Net_18_ROIs_4_lh_native 25 14443610 Net_18_ROIs_5_lh_native 26 10511400 Net_19_ROIs_1_lh_native 27 8323072 Net_2_ROIs_1_lh_native 28 1326300 Net_2_ROIs_2_lh_native 29 3957880 Net_3_ROIs_1_lh_native 30 1316060 Net_3_ROIs_2_lh_native 31 14464220 Net_3_ROIs_3_lh_native 32 8323072 Net_4_ROIs_1_lh_native 33 7874740 Net_5_ROIs_1_lh_native 34 9180300 Net_5_ROIs_2_lh_native 35 8860211 Net_5_ROIs_3_lh_native 36 9182740 Net_5_ROIs_4_lh_native 37 3296035 Net_6_ROIs_1_lh_native 38 9211105 Net_6_ROIs_2_lh_native 39 4924360 Net_6_ROIs_3_lh_native 40 3302560 Net_7_ROIs_1_lh_native 41 3988500 Net_7_ROIs_2_lh_native 42 3988540 Net_8_ROIs_1_lh_native 43 9221340 Net_8_ROIs_2_lh_native 44 3302420 Net_8_ROIs_3_lh_native 45 3302620 Net_8_ROIs_4_lh_native 46 10811612 Net_8_ROIs_5_lh_native 47 2637020 Net_9_ROIs_1_lh_native 48 1326300 Net_9_ROIs_2_lh_native 49 3957880 Net_9_ROIs_3_lh_native Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot

Thanks,

Ben

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On Tue, Jun 14, 2022 at 1:33 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Hi Ben,

I was able to reproduce the core dump. In my case, it was because a mismatch of color scheme between input annotation file and the color table loaded with the surface.

I suspect it might be the same issue for you too. But I’m not sure what the right action is to work around this.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Benjamin Deck Sent: Friday, June 10, 2022 11:47 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi there,

Having issues with the following command:

mri_label2vol --annot lh.yeo_2011.annot --temp /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz --hemi lh --fill-ribbon --identity --subject sub-DAEK --o lh.sub-DAEK_annot_nat.nii.gz

produces the following error:

Number of labels: 0 Annot File: lh.yeo_2011.annot Template Volume: /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz Outut Volume: lh.sub-DAEK_annot_nat.nii.gz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: sub-DAEK Hemi: lh UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects 7.2.0 Template RAS-to-Vox: -------- -1.25000 -0.00000 -0.00000 160.00000; -0.00000 -0.00000 -1.25000 160.00000; -0.00000 1.25000 -0.00000 160.00000; -0.00000 -0.00000 -0.00000 1.00000; Template Voxel Volume: 0.512 nHits Thresh: 0 Using Identity Matrix RegMat: -------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Label RAS-to-Vox: -------- -1.25000 0.00000 0.00000 160.00000; 0.00000 0.00000 -1.25000 160.00000; 0.00000 1.25000 0.00000 160.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.white nvertices = 253237 Reading thickness /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.thickness Loading annotations from lh.yeo_2011.annot annotidmax = 48 nlabels = 48 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgz Mapping Segmentation fault

But when I run the same command without fill-ribbon the process runs to completion.

Not sure if this is a memory issue or something else.

Ben

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University

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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1FUT55eeYf35M-JkMc7UcSX6tQwoolQhFqBp-8LICAUTK0wswJKgW_N0VLBuD8TraBJXxv3A6xEtjOi3zHO6u6hS8qtjCvZLT8blEvNFm05eSJH6b8e3aKqHBqbtFAVOULtn9jgTodt8mPW8m3GmSRUmYpxpu9C3Fkzsso7QpJnn8ogCvZ1glcbo1qzY7f0tbdno7w-kyEgSnfbCNbMMoMyfrKVBy_uY9PmTLYP1fcwc9XbQsn81kFW3GvhlFpwBGRN3Le_la1zqvtr5WRJXwA7glAv3TYsHu2WOT_uygJjXNbYUcMNoxCuIb_tjOc9SD/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/129Kw4R0yoVeTC6bBd1uPUqKUYuQfV-mbD5MR0g-xyo9r99gu2Z-4tY7718A6CVUVsK1u7S1awCDro02sozDsoDFvIHYrhSD5vMlHw_EqisjHZyR11ZdEG2yXwgzu8-sfddrPtz3WvbkujxTvALD-PjFOcUYI_NvZuv-09oniwNIjtKWtpQ32jhSYbp70bpRYQbXH0r71ZqTKS8pYf708p8tjI23a7uEnlutWE573EHFSyZ96N8DYzjiawb99BHqVBLAHIt9CDL5wOEykkXYkYd_eyC6CASQ3k0otyq32qfMyZs0UoWTGjs1OtVTWvtUe/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/129Kw4R0yoVeTC6bBd1uPUqKUYuQfV-mbD5MR0g-xyo9r99gu2Z-4tY7718A6CVUVsK1u7S1awCDro02sozDsoDFvIHYrhSD5vMlHw_EqisjHZyR11ZdEG2yXwgzu8-sfddrPtz3WvbkujxTvALD-PjFOcUYI_NvZuv-09oniwNIjtKWtpQ32jhSYbp70bpRYQbXH0r71ZqTKS8pYf708p8tjI23a7uEnlutWE573EHFSyZ96N8DYzjiawb99BHqVBLAHIt9CDL5wOEykkXYkYd_eyC6CASQ3k0otyq32qfMyZs0UoWTGjs1OtVTWvtUe/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1KFYgeucywv-sgvlszrUVmMExT1D1wTosDU5A-ke32OnzTiJE16BPNnIWUUrRFHCfQlcwzvjB9Q_K1vkrSEJCUQDTLqRHU2UEQjr1vhUytcvG7hKX9glUJjoxbSUY8O_1bQYvpZ7TOKLJ9YXI87fsdsCjOCH8pB3fiIxiezlWu0z6nZe6wVVSJFDrDdBem0x4EW9r5DDygdavp_pb5Y0W7eDFR-iX1WCGnPMNjDjpXexXTIdI_Ol2eLqKWFGHW4MUrUqdaqwYDldwTkGvUFz36lUI7bBBSR8z1QvvqnzPopmvsUdYFcp1-fYYTK9hnrhV/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1KBqYHmYqf-cm-adopQpa1hFDYwc2XxJdOhqXuwG4-p6H_zGJt9CzUb5Bcvty-89vJmkrh4_Y832uL8-DrSaORXDjxvEkwEs8RtxEuQq6lUEUmTfDzlsSL76rkunUEu1FsCKZ4XZ2Wo3E5uXvAb9ZbgagP66-F2BJ-VUqW_2K-K6ArkhyxeOBbFK_7nQsQrvVhi-lxaWl99ahxDwxvyDw0a4G2bKYecYvPx4JDXZOIqOnUJXhrMxb6r-ORsKccILBkvac-C0TUvVDohtWjtbk5SAJgnuIecC_IkYNBNjmdIGPIAtOk50-zSkafZunnfTb/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1KBqYHmYqf-cm-adopQpa1hFDYwc2XxJdOhqXuwG4-p6H_zGJt9CzUb5Bcvty-89vJmkrh4_Y832uL8-DrSaORXDjxvEkwEs8RtxEuQq6lUEUmTfDzlsSL76rkunUEu1FsCKZ4XZ2Wo3E5uXvAb9ZbgagP66-F2BJ-VUqW_2K-K6ArkhyxeOBbFK_7nQsQrvVhi-lxaWl99ahxDwxvyDw0a4G2bKYecYvPx4JDXZOIqOnUJXhrMxb6r-ORsKccILBkvac-C0TUvVDohtWjtbk5SAJgnuIecC_IkYNBNjmdIGPIAtOk50-zSkafZunnfTb/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1pg-D_wLryyZksJTKvQ2XCj2jB5SkB2H8DVHgj5FtQzPyNkniuHdTaL_IBFsxabyNQVwyDAGRDb0cGEIzTIwtcuvIjwV3Lg7QiLDyCU74wL7e7OWYfCCCREmXi9pTrSNypqR7dIGxdS9SqZWfBT2kNZZz3MP8T3iMaDPJB9tUGA0ftI51Y1MpTzJb0BuB7LpTw9riLUlNPvZd3ibg1m7sC629TtuUgdOT-UbH-LxXKgxPhoGJTq0JLzVzIVxqiHbwMlHBsuO84niKNg6mU818Tct_f3UyRX5FTrDYdFHzIsp8PP-5erbf9ISg_MOJtcBAuHtG9F7ocoXiqQITXSSQuw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1ewws5jb1hRDkswPgWMqJP5exouHEKg_qKAlpTyoWlL_21LVGF-OMt6D7Slbg57sQbZwXOVLoDnC9YmdlJJzCPz_HQflF5OSUSoOzRFqBb6S3Zj7jBeo3gp2dpeZTH5IAbvwMwJpAhQONN1708QcTAGvm0HQozK-hXCPgp3gdbe5lVhSGPdR8e1sEZJXq-rZdgdTLIf1a_-e1YvYd5r2ev1HhSuWmyQ5RsQA7Bcb_Rh2TEkdyOmIr0twh52ig6Lrx-_i0r-cciGHcHqmJL_nfrTjOePOVj-htPLFiL1A6BFbEZOUR5-kiUNSZMT9PrStO3fWQUbb7X1WIRA8SBCJQXg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1ewws5jb1hRDkswPgWMqJP5exouHEKg_qKAlpTyoWlL_21LVGF-OMt6D7Slbg57sQbZwXOVLoDnC9YmdlJJzCPz_HQflF5OSUSoOzRFqBb6S3Zj7jBeo3gp2dpeZTH5IAbvwMwJpAhQONN1708QcTAGvm0HQozK-hXCPgp3gdbe5lVhSGPdR8e1sEZJXq-rZdgdTLIf1a_-e1YvYd5r2ev1HhSuWmyQ5RsQA7Bcb_Rh2TEkdyOmIr0twh52ig6Lrx-_i0r-cciGHcHqmJL_nfrTjOePOVj-htPLFiL1A6BFbEZOUR5-kiUNSZMT9PrStO3fWQUbb7X1WIRA8SBCJQXg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1ohxFwDlj95GLWi92_zXWezKzkZSexk4R2BjNZnepB4disZNNuSpW1kK96h-7gzHWzHAfWDFB-dq5WFtrzogG_IDQxfKJM9_8THWm2gTlYr7E4JMzy50EQ0biIxFBc18A7TnYbRKYCW423M2Et_XUa845uEAbuqGRY-rPn8VINSo8n-KcLzZVfZIDWMcJfZiUh7nY6YlsjtlsatA_dXwilbQbksrtIoKDz9rGY5xmZZBLw_VbP8y8YHRyqOrPg4z8ic10lMUnmQgTlmAQ2YgWJ1xKBUPxs5Yk4ek3dLoLkM-g8rkKGlnK7y8aIl9YsPhk/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1gWC8FomBEWvS9SwG5Wk_5Npjvbjt5_29f_qSVE6r4gTYuQr1OZ3heuVWDhm6ygbJNNjl1rcmbLynrODhMW7zGVFOVKJuo9VGT_6ZzY4tD4lpW48h_e3rKiASiRE6iSmhswYQZU3h8c7vDBMokS0is2ROd2vxRcBpVk8R4coPUJm4HAxL7IJkyp9T1IOseEkAQ6Evmgof8igvqcLT9jVdvH6LXAARWQN8TW7ZoIwVtabTajMFOgP-2A0Kg_EmGcDvJqIrVwP2p0e0olstkbXWUkMW1IkROWarolKJ4h73QIjEXEmYKXqsMD_PaNG0quCB/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1gWC8FomBEWvS9SwG5Wk_5Npjvbjt5_29f_qSVE6r4gTYuQr1OZ3heuVWDhm6ygbJNNjl1rcmbLynrODhMW7zGVFOVKJuo9VGT_6ZzY4tD4lpW48h_e3rKiASiRE6iSmhswYQZU3h8c7vDBMokS0is2ROd2vxRcBpVk8R4coPUJm4HAxL7IJkyp9T1IOseEkAQ6Evmgof8igvqcLT9jVdvH6LXAARWQN8TW7ZoIwVtabTajMFOgP-2A0Kg_EmGcDvJqIrVwP2p0e0olstkbXWUkMW1IkROWarolKJ4h73QIjEXEmYKXqsMD_PaNG0quCB/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1-Co0Tj3nO9PKVc4FF5EYp-pbwW1MSBhpVRo4lPgCIr_Le-jinRghImfaUz1XwH3bS9-3JJtGF7iqyCINnenimFyLBFGtPvkx4gKT4LM_XuqtA8yehAilreaW-7tfG7rFm9CKmyvL6UTMUL8ixh3tIeZDVlTa-WL09UQo8OB3xQPLEOyeBBTdvYOD9-EejJcMmPhvCbVyM7VATQc4WnF3BT3C9Wr5Fp2UY25cbOG0IiS9S3TID8jUqddMj_O_8SHKh8odIuW_MNbPu35lVuaMTi9Gh9V0u7p3tOIkH4vOTMN-8GTlTCP5safglQWXvSSt/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1nUKsaivbAuxJojvr0yFs7hY0LXQON0_HrlCUPtW5ymN-QLI0xMSE64vbmxo74tTH5VaFyluU46uvw3l-Oi9Zs6J_C9ApmKC6YBCM7Vp9dxkgV2G-JQiYfsxps_neYqUYs3Ex6cqTkpvxd29lBZXFfOAAEuEh89KJ9t3RbBTeOlzXr_mxGPrA9_wXx5Ik_NMVLgPT_qhUj3n03BUZBWoYAS8fR1HG-dDJAvMSNEIbB4DEEaIO1w4toFS_NkYAtb0_kF5ch2aEyPtKeAXZXAQNHORaUhvK4OmoxzwZuVrxEFBj3kjicTmAplnxy8Ns7pjx/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1nUKsaivbAuxJojvr0yFs7hY0LXQON0_HrlCUPtW5ymN-QLI0xMSE64vbmxo74tTH5VaFyluU46uvw3l-Oi9Zs6J_C9ApmKC6YBCM7Vp9dxkgV2G-JQiYfsxps_neYqUYs3Ex6cqTkpvxd29lBZXFfOAAEuEh89KJ9t3RbBTeOlzXr_mxGPrA9_wXx5Ik_NMVLgPT_qhUj3n03BUZBWoYAS8fR1HG-dDJAvMSNEIbB4DEEaIO1w4toFS_NkYAtb0_kF5ch2aEyPtKeAXZXAQNHORaUhvK4OmoxzwZuVrxEFBj3kjicTmAplnxy8Ns7pjx/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1vY_16Zjww2xu0uzWyiUohSSGGRD2H3nPfBx-WboNIK-KoK15rtSqkX2N-vmZ_cZ27ff2CpMOXLf512LEyZ_evkkY3h5Fj3fd8kZmWMbNzbz13qEX-J_IC_P6asO8e2VQ_smAoIOlIkFkOJHjdqGr04XT2bVWuPZjC9dOlUH26F47LauKhAEPdxCKLr4NE9Pv3ivq0eZZ5kFH0bqLzGyz0nNRpBvXgkwvnlq8hqiHZ8Bxe0h2o9TE0GEYSMPGRmj3BKHyBYVGLsX58dmumT-cSW8AEvkCb91oK2Lv-DywOJBySAA4UnwaUtsPVsa-Qaz80DhUEKpRssMKaD0KwpO1-Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1KyPIPmRNwus-z79lEGn0T7diD2lNJqoI2KIQh4lMv2faOIlvJOXCKLsN35WtRkxw61rareTh_XeaqS274mShL_BwFF0zrupuNsCOKEU94cyu7wYoAM6A93LTuYfY69rB1_3laFePNZaecZtHzcaAqoooOI2HEKJu89TZc6ronKly_Y7oIPveyaULOt3u4wFYCT2PowbhyLRJ5rEfGIkGksjlIxIB46ynWAQuDbi1KJPj7YPc039Tros_bYxNL_UjuGzrk_VVjobmcicqBvJbHh69MPWijPmHDSLTSx76IPcDo85-lkMmm_-3yhZXEoMMFwMXN-kGs8rg9zY0wYgyNQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1KyPIPmRNwus-z79lEGn0T7diD2lNJqoI2KIQh4lMv2faOIlvJOXCKLsN35WtRkxw61rareTh_XeaqS274mShL_BwFF0zrupuNsCOKEU94cyu7wYoAM6A93LTuYfY69rB1_3laFePNZaecZtHzcaAqoooOI2HEKJu89TZc6ronKly_Y7oIPveyaULOt3u4wFYCT2PowbhyLRJ5rEfGIkGksjlIxIB46ynWAQuDbi1KJPj7YPc039Tros_bYxNL_UjuGzrk_VVjobmcicqBvJbHh69MPWijPmHDSLTSx76IPcDo85-lkMmm_-3yhZXEoMMFwMXN-kGs8rg9zY0wYgyNQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1d-XvOBTFt5_cCa1ye5yP05mcuegypNqJsB3YldmgVm9hZXlDDibihHBqSKyDfeehlS21WDHZXaBMcoCdXnm5IVkryRuuJ8wT_F5O4WKKW-nGCoQOeBL8NHUVbDS5rRZyi8H-LK1Hk7GtktvC7uI8POxnmeO2lU9IKErk5C4myGVZ-k2S8cEh7b60xI-j7T6IL-Yw3T5u39s8iS_1YXo_b5WcDqJRcyVYHI8WIO6OD-77ZSfgiAjNBq6MKK1g8OVXGh7qmULSfQbWxkw2EqAHDRCfND_WrNdwmDynVgAgVjacWzqzEFH5cNyYzTdjzoIb/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1yZ4R709Tjj8VA5gFKY9oVtxWsJzJH7HEA1mWR8DhG1nRvJUL95yflD16xZbNnBl7Bg_W_ICi2nSVtpLaRp2L9SLjeSr0cII31PajLLxMoLLibjNweV73icSWZ0BUw5SrQEFk64BQHu627ftWSiYuxiM8OJw2G8sEjnOIVnc7fwGGCqQ4SGDTQOZqTm6-FeOLz6oBlgGqAIrvxm5fOKMi03ARCrsgT6NFhTNZRFPZb0tMuQ_5uFSQ2WPuXEJFK1XQfasgF8r-wWmWkoTeHt-B21bHxypJiWSVFWxIEcockJbHk7ZgSb4yd4BBbuEHIRpU/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1yZ4R709Tjj8VA5gFKY9oVtxWsJzJH7HEA1mWR8DhG1nRvJUL95yflD16xZbNnBl7Bg_W_ICi2nSVtpLaRp2L9SLjeSr0cII31PajLLxMoLLibjNweV73icSWZ0BUw5SrQEFk64BQHu627ftWSiYuxiM8OJw2G8sEjnOIVnc7fwGGCqQ4SGDTQOZqTm6-FeOLz6oBlgGqAIrvxm5fOKMi03ARCrsgT6NFhTNZRFPZb0tMuQ_5uFSQ2WPuXEJFK1XQfasgF8r-wWmWkoTeHt-B21bHxypJiWSVFWxIEcockJbHk7ZgSb4yd4BBbuEHIRpU/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1lzAEnfma6POriv_9X0wlCvWy5HKVOhCMMb6Py23KTy7VQudt92j3AChBm4bOXncxPhREzceez-te1VuGynFrHbVDfWwOctA075a43xwe8tEAWwZ9RkQz6m-aafxFHAgqrBafsWpk0fzWmogyMVOSRsels8hwd1rp31dHUilMZW_Dk3B4xPIRHwtOBa8Tyi5oXeQpBVjhPHfR4HFqFrMY7Ep6rR9a0sqmYJxY_jGECBk-vCAY6PDYPOWIveda7-1Z-VS9qjQTR324dTl-f8EWW3eEEgyc14E3rQzUv7_-P6xsBa9ZaeNu_yHqOUJDy4gnkqW-qGCSFpbGbvA7PJUhug/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1VDVDYXIA1BawsJs6pGa6PJQLtxlKlhJ1ZlRQdtc02cQ2tzIse4MfZuUh4JBnlpViJACS_xbhnrWZwfyPcUQllldVl9U82FiEz9o458oONw_n7W6Ipwkwfg_zSUAhZ_GcmD1QOoyvGzBGOS6hRn7YJn9WkS3NEYxPs9ycS6UsOJ088NANy1nOBB70UA7wjGro_K4fDlqCkFXAoh5MYYy-LqKEytpcaTSdk5aUwsaYUYqu4ALPN0qwlRXmIhO1gptEKr6d2srJpRWFkNAhbFC9D_nySMtkc-71QNo0T8cn6p3z1PyDGKMD8QPi6LrMXYqjMEtv0zGsDYVA3oL0IJ3_BQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1VDVDYXIA1BawsJs6pGa6PJQLtxlKlhJ1ZlRQdtc02cQ2tzIse4MfZuUh4JBnlpViJACS_xbhnrWZwfyPcUQllldVl9U82FiEz9o458oONw_n7W6Ipwkwfg_zSUAhZ_GcmD1QOoyvGzBGOS6hRn7YJn9WkS3NEYxPs9ycS6UsOJ088NANy1nOBB70UA7wjGro_K4fDlqCkFXAoh5MYYy-LqKEytpcaTSdk5aUwsaYUYqu4ALPN0qwlRXmIhO1gptEKr6d2srJpRWFkNAhbFC9D_nySMtkc-71QNo0T8cn6p3z1PyDGKMD8QPi6LrMXYqjMEtv0zGsDYVA3oL0IJ3_BQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/12mn7RrjCSk9wKN2bkmYBOEFx55ZtxmS03S3iVl-uRN6nphxIL6CcOGbHZuUak1DgehJMaf2YrCkP9UiYgAGoMu_nHjP5DbznmqoNNjHZN3nd5YNgDkuIJZCZ7_4b8yi4gkIN8-hB65W0IrRTSyTlx8ylE45lDqEhW2FMWqriCj8Nf0ZuUOybHcpr-rFgMa_JV9FkRzasQZU82NfiPm6MRYqO7YravhAPqK2tr_bjS9PBMjAuaRJuAet754OEKaTMzCqdokYoBISmWfMZatmFZGc4A-EbudAoP6jhQNWR3SK-F2XAT-wr8L9syzYaOKTttNhOHVvrCpNbjDgsbo0-WQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/18rTAG60ckLxswQJOuBlSj0VR07O1sNVbgYouhGBkuOy5laLgNBLagNMGll788px3_tkhFpGXW-JV52PcTf-zCb0Hf9IHz0zLiT--UyoWLs416q5jMEmVBQ46pafdgrS5XT60rkBkQ8WMJ0WVAijGSXffi1Mlr8umYJXzuvLxPXp5U6NdwWfEUBw0RzrbEpD1mjD1maN0Inxi4OYQHZhk_s-bjeebKOMnQhunjN7vp2IokhDS6YkAst6z4JdN9MHVSCF2ahw8y52KVQVvF3R2Jmzc0ILYBWQWikSshZQMSlbcDZ4WL1ZTedxqSws74DqIUjQI2AMqlslY_TVrgoN3mQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/18rTAG60ckLxswQJOuBlSj0VR07O1sNVbgYouhGBkuOy5laLgNBLagNMGll788px3_tkhFpGXW-JV52PcTf-zCb0Hf9IHz0zLiT--UyoWLs416q5jMEmVBQ46pafdgrS5XT60rkBkQ8WMJ0WVAijGSXffi1Mlr8umYJXzuvLxPXp5U6NdwWfEUBw0RzrbEpD1mjD1maN0Inxi4OYQHZhk_s-bjeebKOMnQhunjN7vp2IokhDS6YkAst6z4JdN9MHVSCF2ahw8y52KVQVvF3R2Jmzc0ILYBWQWikSshZQMSlbcDZ4WL1ZTedxqSws74DqIUjQI2AMqlslY_TVrgoN3mQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

-- Benjamin L. Deck Doctoral Student Applied Cognitive and Brain Sciences Department of Psychological and Brain Sciences Drexel University